Variant report

Variant	rs4980813
Chromosome Location	chr12:414287-414288
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10744616	0.84[EUR][1000 genomes]
rs10774150	0.84[EUR][1000 genomes]
rs10848715	0.93[EUR][1000 genomes]
rs10848716	0.93[EUR][1000 genomes]
rs11062302	0.90[EUR][1000 genomes]
rs11062385	0.94[EUR][1000 genomes]
rs11608938	0.87[AMR][1000 genomes]
rs11611810	0.93[EUR][1000 genomes]
rs1207322	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1207323	0.86[EUR][1000 genomes]
rs12582850	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17800744	0.80[AMR][1000 genomes]
rs1860360	0.83[EUR][1000 genomes]
rs2052279	0.89[EUR][1000 genomes]
rs2159364	0.82[EUR][1000 genomes]
rs2229351	0.91[EUR][1000 genomes]
rs2284332	0.89[EUR][1000 genomes]
rs3213751	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3753157	0.88[EUR][1000 genomes]
rs3753158	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3815558	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs495316	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4980814	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4980875	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4980876	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4980877	0.81[EUR][1000 genomes]
rs4980878	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4980883	0.83[EUR][1000 genomes]
rs4980884	0.88[EUR][1000 genomes]
rs4980885	0.86[EUR][1000 genomes]
rs507597	0.80[AMR][1000 genomes]
rs525381	0.90[EUR][1000 genomes]
rs57022939	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576159	0.87[EUR][1000 genomes]
rs576994	0.89[EUR][1000 genomes]
rs61906995	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61906996	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61907027	0.91[EUR][1000 genomes]
rs6489450	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7134353	0.81[EUR][1000 genomes]
rs7135768	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7298019	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7301422	0.85[EUR][1000 genomes]
rs7303180	0.81[EUR][1000 genomes]
rs764614	0.80[EUR][1000 genomes]
rs7963309	0.80[EUR][1000 genomes]
rs7977462	0.82[EUR][1000 genomes]
rs797759	0.89[EUR][1000 genomes]
rs7979745	0.83[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	nsv1046121	chr12:282465-416134	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv531957	chr12:282465-465789	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1049579	chr12:282465-471163	Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv1054973	chr12:296179-464439	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv541321	chr12:296179-464439	Weak transcription Strong transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	nsv898564	chr12:368476-415056	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
30	esv34939	chr12:371786-433151	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
31	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
32	nsv819688	chr12:406038-415530	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4980813	CCDC77	cis	Artery Tibial	GTEx
rs4980813	CCDC77	cis	Thyroid	GTEx
rs4980813	JARID1A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:384600-414600	Weak transcription	Psoas Muscle	Psoas
2	chr12:389400-455200	Strong transcription	Primary B cells from peripheral blood	blood
3	chr12:394000-474400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:394800-414800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:395000-416200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:398200-416000	Weak transcription	Stomach Mucosa	stomach
7	chr12:400800-440800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:402000-427200	Weak transcription	K562	blood
9	chr12:402200-414400	Weak transcription	Fetal Brain Male	brain
10	chr12:402200-415400	Weak transcription	Pancreas	Pancrea
11	chr12:404800-414800	Weak transcription	Gastric	stomach
12	chr12:404800-415600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:405000-414600	Weak transcription	Esophagus	oesophagus
14	chr12:405000-414600	Weak transcription	Right Ventricle	heart
15	chr12:405000-414800	Weak transcription	Aorta	Aorta
16	chr12:405000-414800	Weak transcription	Spleen	Spleen
17	chr12:405000-416600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:405400-414800	Weak transcription	Lung	lung
19	chr12:405400-415200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:405400-416000	Weak transcription	NHLF	lung
21	chr12:405600-415200	Weak transcription	Fetal Intestine Small	intestine
22	chr12:405600-415600	Weak transcription	Colonic Mucosa	Colon
23	chr12:406200-414600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:406400-414600	Weak transcription	NHEK	skin
25	chr12:406400-416000	Weak transcription	HSMMtube	muscle
26	chr12:406800-416000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr12:406800-416000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr12:407000-415600	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:407200-414800	Weak transcription	HUVEC	blood vessel
30	chr12:407600-415000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:407600-415400	Weak transcription	Ovary	ovary
32	chr12:407800-415000	Weak transcription	Fetal Stomach	stomach
33	chr12:407800-416600	Weak transcription	Small Intestine	intestine
34	chr12:408600-415200	Weak transcription	Brain Anterior Caudate	brain
35	chr12:408800-414600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:409400-439000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:409800-451600	Strong transcription	Fetal Thymus	thymus
38	chr12:410600-419400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr12:411400-433600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:411600-424000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:411600-438600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr12:411600-448000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:411600-450800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:411600-453800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr12:412000-423000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr12:412000-428000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:412000-431000	Strong transcription	Liver	Liver
48	chr12:412000-433400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:412000-435800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:412000-438200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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