Variant report

Variant	rs10744616
Chromosome Location	chr12:489205-489206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:488968..490712-chr12:497347..499213,2	MCF-7	breast:
2	chr12:486737..489669-chr12:496897..500198,3	K562	blood:
3	chr12:486794..489246-chr12:492841..495214,2	K562	blood:
4	chr12:488452..493838-chr12:496746..499307,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000073614	Chromatin interaction
ENSG00000120647	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1011699	0.84[AMR][1000 genomes]
rs10431354	0.86[EUR][1000 genomes]
rs10431355	0.93[EUR][1000 genomes]
rs10735021	0.93[EUR][1000 genomes]
rs10744627	0.84[ASN][1000 genomes]
rs10774137	0.85[EUR][1000 genomes]
rs10774150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10774153	0.80[EUR][1000 genomes]
rs10774154	0.87[AMR][1000 genomes]
rs10774170	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10848838	0.91[EUR][1000 genomes]
rs10848845	0.93[EUR][1000 genomes]
rs10848849	0.85[EUR][1000 genomes]
rs10848868	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10848879	0.93[EUR][1000 genomes]
rs11062803	0.87[ASN][1000 genomes]
rs1155942	0.84[AMR][1000 genomes]
rs12582850	0.83[EUR][1000 genomes]
rs1541464	0.95[ASN][1000 genomes]
rs1541465	0.95[ASN][1000 genomes]
rs1860360	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041299	0.87[AMR][1000 genomes]
rs2098094	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2159364	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253565	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2300133	0.88[EUR][1000 genomes]
rs2300134	0.91[EUR][1000 genomes]
rs2369276	0.93[EUR][1000 genomes]
rs2369277	0.95[ASN][1000 genomes]
rs3213751	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3753158	0.82[ASN][1000 genomes]
rs3759371	0.90[EUR][1000 genomes]
rs3782852	0.91[EUR][1000 genomes]
rs3815558	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4482086	0.85[ASN][1000 genomes]
rs4980813	0.84[EUR][1000 genomes]
rs4980814	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4980817	0.84[ASN][1000 genomes]
rs4980876	0.84[EUR][1000 genomes]
rs4980878	0.83[EUR][1000 genomes]
rs4980883	0.81[EUR][1000 genomes]
rs4980884	0.86[EUR][1000 genomes]
rs4980885	0.83[EUR][1000 genomes]
rs61906996	0.84[EUR][1000 genomes]
rs6489448	0.89[EUR][1000 genomes]
rs6489449	0.92[EUR][1000 genomes]
rs6489450	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6489454	0.93[EUR][1000 genomes]
rs6489458	0.93[EUR][1000 genomes]
rs6489471	0.93[EUR][1000 genomes]
rs6489475	0.87[AMR][1000 genomes]
rs6489477	0.94[EUR][1000 genomes]
rs6489478	0.92[EUR][1000 genomes]
rs7132763	0.80[EUR][1000 genomes]
rs7133796	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7134608	0.93[EUR][1000 genomes]
rs7135768	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7136957	0.93[EUR][1000 genomes]
rs7138890	0.93[EUR][1000 genomes]
rs7138981	0.80[EUR][1000 genomes]
rs715228	0.88[EUR][1000 genomes]
rs715229	0.88[EUR][1000 genomes]
rs715230	0.88[EUR][1000 genomes]
rs7298019	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7298995	0.80[EUR][1000 genomes]
rs7301422	0.83[EUR][1000 genomes]
rs7311496	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7312065	0.87[EUR][1000 genomes]
rs7316660	0.91[EUR][1000 genomes]
rs7953137	0.93[EUR][1000 genomes]
rs7965038	0.87[AMR][1000 genomes]
rs7965303	0.93[EUR][1000 genomes]
rs7972566	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7977462	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979745	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949498	chr12:282465-493900	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1051726	chr12:282465-511843	Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv541304	chr12:282465-635505	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1042991	chr12:282465-666255	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1041574	chr12:282465-812000	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv541305	chr12:282465-1016828	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
7	nsv869390	chr12:282465-1045994	Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
9	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv1050781	chr12:321353-783899	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv1040849	chr12:321619-771493	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv541322	chr12:321619-771493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
13	nsv1035679	chr12:321619-781558	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv1053519	chr12:321619-828175	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
15	nsv1044433	chr12:321619-1065402	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
16	nsv541323	chr12:321619-1065402	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
17	nsv898563	chr12:332860-493900	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	esv2757484	chr12:335010-543206	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
19	esv2759875	chr12:335010-990544	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
20	nsv1045638	chr12:349031-893536	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
21	nsv541325	chr12:349031-893536	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
22	nsv1050646	chr12:362398-658665	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
23	nsv541326	chr12:362398-658665	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
24	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
25	nsv898565	chr12:428131-564185	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
26	nsv1052201	chr12:429128-515675	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
27	nsv541328	chr12:429128-515675	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
28	nsv442250	chr12:432808-543847	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
29	esv2756520	chr12:433151-543206	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
30	nsv1050226	chr12:441032-743195	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
31	nsv1035222	chr12:449993-515675	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
32	esv2758290	chr12:457433-990544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10744616	CCDC77	cis	Artery Tibial	GTEx
rs10744616	JARID1A	Cis_1M	lymphoblastoid	RTeQTL
rs10744616	CCDC77	cis	Thyroid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:474600-492600	Weak transcription	NHEK	skin
2	chr12:474800-492800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:474800-495200	Weak transcription	Fetal Heart	heart
4	chr12:475200-496800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:483600-493600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:484000-493400	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr12:484000-494000	Strong transcription	Adipose Nuclei	Adipose
8	chr12:484000-494200	Strong transcription	Thymus	Thymus
9	chr12:484000-494400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:484200-494000	Strong transcription	Primary B cells from peripheral blood	blood
11	chr12:484200-494400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:484400-489400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr12:484400-489600	Strong transcription	Brain Cingulate Gyrus	brain
14	chr12:484400-489800	Strong transcription	Colon Smooth Muscle	Colon
15	chr12:484400-492400	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr12:484400-493000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:484400-493400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr12:484400-493600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:484400-493800	Strong transcription	Primary T cells from cord blood	blood
20	chr12:484400-494000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:484400-494000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:484400-494000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr12:484400-494000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:484400-494000	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:484400-494200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr12:484400-494200	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr12:484400-494200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:484400-494200	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr12:484400-494400	Strong transcription	Liver	Liver
30	chr12:484400-494800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:484400-494800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:484400-494800	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr12:484400-494800	Strong transcription	Primary B cells from cord blood	blood
34	chr12:484400-494800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr12:484400-495000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:484400-495000	Strong transcription	Fetal Thymus	thymus
37	chr12:484400-495200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:484600-489600	Strong transcription	NHLF	lung
39	chr12:484600-492000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:484600-493600	Strong transcription	Fetal Kidney	kidney
41	chr12:484600-493600	Strong transcription	Ovary	ovary
42	chr12:484600-493800	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:484600-494000	Strong transcription	Placenta	Placenta
44	chr12:484600-494000	Strong transcription	NH-A	brain
45	chr12:484600-494200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr12:484600-494400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr12:484600-495000	Strong transcription	A549	lung
48	chr12:484800-494200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:484800-494200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr12:484800-494200	Strong transcription	Osteobl	bone

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