Variant report

Variant	rs10774169
Chromosome Location	chr12:516346-516347
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:515684..517646-chr12:519999..522840,2	K562	blood:
2	chr12:509480..512671-chr12:512718..518002,7	K562	blood:
3	chr12:509245..512944-chr12:513140..518002,8	K562	blood:

Variant related genes	Relation type
ENSG00000120647	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10774152	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10774153	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10774163	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10774170	0.94[CEU][hapmap]
rs10848814	0.84[ASN][1000 genomes]
rs10848905	1.00[CEU][hapmap];0.93[GIH][hapmap];0.81[EUR][1000 genomes]
rs1155942	0.94[CEU][hapmap]
rs1207322	0.84[CEU][hapmap]
rs12311569	0.83[ASN][1000 genomes]
rs12581260	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12582850	0.84[CEU][hapmap]
rs1541462	0.94[EUR][1000 genomes]
rs1541463	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1541464	0.94[CEU][hapmap];0.83[GIH][hapmap]
rs1541465	0.94[CEU][hapmap]
rs16929783	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1860360	0.84[CEU][hapmap]
rs2007537	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2015554	0.85[ASN][1000 genomes]
rs2300131	0.84[ASN][1000 genomes]
rs2369280	0.89[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs3213750	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3815558	0.84[CEU][hapmap]
rs486098	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs495316	0.89[CEU][hapmap]
rs4980814	0.84[CEU][hapmap]
rs4980874	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs4980877	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs4980881	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4980883	0.90[CEU][hapmap];0.91[CHB][hapmap]
rs4980885	0.90[CEU][hapmap];0.91[CHB][hapmap];0.84[MEX][hapmap]
rs4980886	0.85[ASN][1000 genomes]
rs4980892	0.84[EUR][1000 genomes]
rs520932	0.84[CEU][hapmap]
rs524468	0.84[CEU][hapmap];0.80[MEX][hapmap]
rs525381	0.84[CEU][hapmap]
rs541273	0.87[CHB][hapmap]
rs579526	0.84[CEU][hapmap];0.84[MEX][hapmap]
rs7132763	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7132845	0.86[ASN][1000 genomes]
rs7134353	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap]
rs7136957	0.90[CEU][hapmap]
rs7138958	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7138981	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs720128	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7298019	0.84[CEU][hapmap]
rs7298995	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7301422	0.90[CEU][hapmap];0.91[CHB][hapmap];0.84[MEX][hapmap]
rs7315852	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs7953137	0.90[CEU][hapmap];0.87[CHB][hapmap];0.84[MEX][hapmap]
rs797765	0.84[CEU][hapmap]
rs887311	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	nsv949226	chr12:493900-814882	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
28	nsv898566	chr12:499041-570917	Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
29	nsv1036822	chr12:504573-586674	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
30	nsv541329	chr12:504573-586674	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
31	nsv514668	chr12:506474-521532	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10774169	CCDC77	cis	cerebellum	SCAN
rs10774169	CCDC77	cis	parietal	SCAN
rs10774169	CCDC77	cis	Artery Tibial	GTEx
rs10774169	JARID1A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:511200-519600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:511200-521000	Weak transcription	Lung	lung
3	chr12:511200-521000	Weak transcription	Spleen	Spleen
4	chr12:511200-521400	Weak transcription	Gastric	stomach
5	chr12:511200-521400	Weak transcription	Pancreas	Pancrea
6	chr12:511400-521000	Weak transcription	Left Ventricle	heart
7	chr12:511400-521200	Weak transcription	Ovary	ovary
8	chr12:511400-521600	Weak transcription	Aorta	Aorta
9	chr12:511600-519600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr12:511600-519800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:511600-519800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:511600-520800	Weak transcription	Right Ventricle	heart
13	chr12:511600-521000	Weak transcription	Placenta	Placenta
14	chr12:511600-521200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:511600-521400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:511600-521400	Weak transcription	Esophagus	oesophagus
17	chr12:511600-523600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:511600-544600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:511800-519600	Weak transcription	Fetal Muscle Leg	muscle
20	chr12:511800-519600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:511800-519800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:511800-520800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr12:511800-520800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr12:511800-520800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr12:511800-520800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:511800-520800	Weak transcription	Adipose Nuclei	Adipose
27	chr12:511800-520800	Weak transcription	Liver	Liver
28	chr12:511800-520800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:511800-520800	Weak transcription	Fetal Thymus	thymus
30	chr12:511800-520800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:511800-521000	Weak transcription	Brain Substantia Nigra	brain
32	chr12:511800-521000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr12:511800-521200	Weak transcription	Brain Anterior Caudate	brain
34	chr12:511800-522600	Weak transcription	Colonic Mucosa	Colon
35	chr12:511800-523600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:511800-523800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr12:511800-523800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:511800-524000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:512000-518600	Weak transcription	Fetal Intestine Small	intestine
40	chr12:512000-519600	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:512000-520000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr12:512000-520600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr12:512000-520800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:512000-520800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr12:512000-520800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:512000-521000	Weak transcription	Primary B cells from peripheral blood	blood
47	chr12:512000-521000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr12:512000-521000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr12:512000-521000	Weak transcription	Fetal Intestine Large	intestine
50	chr12:512000-521200	Weak transcription	Brain Angular Gyrus	brain

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