Variant report

Variant	rs3736466
Chromosome Location	chr12:39756878-39756879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39752339..39754010-chr12:39754627..39757326,2	K562	blood:
2	chr12:39748533..39750921-chr12:39755964..39757616,2	K562	blood:
3	chr12:39747712..39750921-chr12:39754829..39757616,3	K562	blood:
4	chr12:39751967..39753839-chr12:39754682..39757326,2	K562	blood:
5	chr12:39755090..39757754-chr12:39764621..39766612,2	MCF-7	breast:
6	chr12:39756404..39758819-chr12:39835044..39837136,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139116	Chromatin interaction
ENSG00000252974	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10876868	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876876	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876886	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876972	0.84[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs11171674	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171676	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171720	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11171730	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171901	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171923	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171938	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172108	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11172120	0.84[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs11172183	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs11172282	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11172492	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs11172592	0.94[JPT][hapmap]
rs11830643	0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11836755	0.94[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs12228767	0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12230604	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424345	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1512936	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1512941	0.81[ASW][hapmap]
rs1512942	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1567739	0.84[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17127019	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1828653	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1955314	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2388320	0.84[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4284427	0.88[JPT][hapmap]
rs4320988	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs4492858	0.84[CEU][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs4500523	0.86[GIH][hapmap];0.95[JPT][hapmap]
rs57756176	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57833783	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59695906	0.82[ASN][1000 genomes]
rs60792848	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7137143	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953548	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7962283	0.83[CEU][hapmap]
rs7964447	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7968837	0.84[CEU][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs7971515	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7974928	0.81[ASW][hapmap];0.91[CEU][hapmap];0.81[CHB][hapmap];0.89[GIH][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap]
rs7976275	0.81[ASW][hapmap]
rs7979329	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7979444	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[ASN][1000 genomes]
rs958914	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832375	chr12:39599362-39784722	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv558589	chr12:39667861-39768356	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39696600-39762200	Weak transcription	Fetal Brain Male	brain
2	chr12:39697800-39771800	Weak transcription	Fetal Kidney	kidney
3	chr12:39699600-39760600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:39721000-39770600	Weak transcription	Gastric	stomach
5	chr12:39722800-39767200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:39726400-39766600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr12:39726600-39766600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:39726600-39766600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr12:39726600-39766800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:39726800-39762200	Weak transcription	Placenta	Placenta
11	chr12:39726800-39766600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:39727000-39758000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:39727000-39758000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr12:39727000-39758200	Weak transcription	Fetal Intestine Large	intestine
15	chr12:39727000-39760600	Weak transcription	Brain Angular Gyrus	brain
16	chr12:39727000-39761400	Weak transcription	Fetal Intestine Small	intestine
17	chr12:39727000-39762400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:39727000-39767000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:39727000-39779200	Weak transcription	Aorta	Aorta
20	chr12:39735200-39761400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr12:39735600-39766600	Weak transcription	HMEC	breast
22	chr12:39735600-39766600	Weak transcription	NHEK	skin
23	chr12:39737400-39766600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:39740600-39761200	Weak transcription	Brain Substantia Nigra	brain
25	chr12:39742600-39761400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr12:39743000-39766800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:39743200-39765800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:39745000-39762000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:39745000-39778600	Weak transcription	Pancreas	Pancrea
30	chr12:39748200-39764000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:39748400-39765800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr12:39748800-39764000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:39749000-39764200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:39749800-39761200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:39750200-39761600	Weak transcription	Small Intestine	intestine
36	chr12:39750200-39765400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:39750400-39762000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:39750600-39760000	Weak transcription	Hela-S3	cervix
39	chr12:39750600-39760400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr12:39750800-39762200	Weak transcription	HepG2	liver
41	chr12:39751200-39759600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr12:39751200-39761200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:39751200-39762400	Weak transcription	Adipose Nuclei	Adipose
44	chr12:39751200-39762600	Weak transcription	K562	blood
45	chr12:39751400-39758200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:39751400-39770400	Weak transcription	Brain Hippocampus Middle	brain
47	chr12:39751600-39757200	Weak transcription	Esophagus	oesophagus
48	chr12:39751600-39771800	Weak transcription	Brain Anterior Caudate	brain
49	chr12:39752000-39765400	Weak transcription	Left Ventricle	heart
50	chr12:39752200-39760400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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