Variant report

Variant	rs12764662
Chromosome Location	chr10:116722834-116722835
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:116718109..116720528-chr10:116722759..116724977,2	K562	blood:
2	chr10:116721231..116723812-chr10:116727155..116729844,2	K562	blood:
3	chr10:116722299..116723812-chr10:116727808..116729844,2	K562	blood:

Variant related genes	Relation type
ENSG00000252611	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10160015	0.90[ASN][1000 genomes]
rs10444099	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1045657	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490908	1.00[JPT][hapmap]
rs10510008	0.81[ASN][1000 genomes]
rs10885632	0.81[ASN][1000 genomes]
rs10885633	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10885634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10885636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10885637	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs10885638	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10885639	1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11196983	0.81[ASN][1000 genomes]
rs11196984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11196989	0.81[ASN][1000 genomes]
rs11196991	0.95[ASN][1000 genomes]
rs11196996	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11196999	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11197000	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11197005	0.95[ASN][1000 genomes]
rs11197006	0.87[ASN][1000 genomes]
rs11197007	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11197010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11197011	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs11197012	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11197023	1.00[ASN][1000 genomes]
rs12098332	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12246008	1.00[ASN][1000 genomes]
rs12265048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12269261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12761122	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12772737	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774597	1.00[ASN][1000 genomes]
rs12775180	1.00[JPT][hapmap]
rs12779231	1.00[ASN][1000 genomes]
rs17092542	1.00[JPT][hapmap]
rs17721283	1.00[JPT][hapmap]
rs17721905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17722042	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17794346	1.00[JPT][hapmap]
rs17795104	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795212	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1966384	1.00[JPT][hapmap]
rs2095379	0.95[ASN][1000 genomes]
rs2105001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2420070	0.81[ASN][1000 genomes]
rs34170154	1.00[ASN][1000 genomes]
rs34434610	1.00[ASN][1000 genomes]
rs34453431	1.00[ASN][1000 genomes]
rs34461950	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35501899	1.00[ASN][1000 genomes]
rs35811923	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3931556	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs61869271	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869272	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869274	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869275	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6585302	0.81[ASN][1000 genomes]
rs6585306	0.95[ASN][1000 genomes]
rs6585309	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6585310	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6585311	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6585313	1.00[ASN][1000 genomes]
rs7071789	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7071812	1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7072356	1.00[JPT][hapmap]
rs7074729	1.00[JPT][hapmap]
rs7075888	1.00[JPT][hapmap]
rs7079234	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7085964	0.90[ASN][1000 genomes]
rs7093282	0.87[ASN][1000 genomes]
rs7093330	1.00[ASN][1000 genomes]
rs7094072	1.00[JPT][hapmap]
rs7097580	1.00[ASN][1000 genomes]
rs7099565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7099590	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7099779	0.95[ASN][1000 genomes]
rs7100026	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100159	0.95[ASN][1000 genomes]
rs7100894	0.81[ASN][1000 genomes]
rs72836518	1.00[ASN][1000 genomes]
rs749649	1.00[JPT][hapmap]
rs7895551	1.00[JPT][hapmap]
rs7898249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7904605	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7908069	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7908464	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7909566	1.00[JPT][hapmap]
rs7909657	1.00[JPT][hapmap]
rs7917523	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs7923295	1.00[JPT][hapmap]
rs881192	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs968848	1.00[ASN][1000 genomes]
rs968849	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS 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 miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv831996	chr10:116601552-116772968	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1039002	chr10:116643095-116879483	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv2761634	chr10:116643095-116879495	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv1045654	chr10:116654574-116879483	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1043242	chr10:116655057-116883386	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv831997	chr10:116689552-116855698	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12764662	TRUB1	Cis_1M	lymphoblastoid	RTeQTL
rs12764662	TCF7L2	cis	cerebellum	SCAN
rs12764662	ADRB1	cis	parietal	SCAN
rs12764662	ATRNL1	cis	Muscle Skeletal	GTEx
rs12764662	TRUB1	cis	cerebellum	SCAN
rs12764662	TRUB1	cis	parietal	SCAN
rs12764662	TECTB	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116698800-116730400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:116698800-116763600	Weak transcription	Esophagus	oesophagus
3	chr10:116699600-116736400	Weak transcription	NHLF	lung
4	chr10:116699800-116726200	Weak transcription	K562	blood
5	chr10:116703400-116730400	Weak transcription	Pancreas	Pancrea
6	chr10:116703600-116740800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr10:116703600-116747800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr10:116705000-116728000	Weak transcription	Small Intestine	intestine
9	chr10:116705400-116735400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr10:116705400-116739400	Weak transcription	Thymus	Thymus
11	chr10:116705600-116728000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr10:116705800-116724600	Weak transcription	Colonic Mucosa	Colon
13	chr10:116705800-116730400	Weak transcription	Placenta	Placenta
14	chr10:116706000-116723600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr10:116706000-116729400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr10:116707000-116744200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr10:116707000-116745600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr10:116708800-116742000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr10:116709200-116726400	Weak transcription	HUVEC	blood vessel
20	chr10:116710800-116741200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr10:116711800-116733000	Weak transcription	Hela-S3	cervix
22	chr10:116712600-116730400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr10:116713800-116734200	Weak transcription	Psoas Muscle	Psoas
24	chr10:116714200-116739400	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr10:116716400-116743200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr10:116717200-116730200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr10:116718000-116730200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr10:116718000-116737400	Weak transcription	NHDF-Ad	bronchial
29	chr10:116718000-116747600	Weak transcription	Osteobl	bone
30	chr10:116718800-116723000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:116718800-116723600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr10:116719000-116723200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr10:116719000-116724200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr10:116719200-116723200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:116719200-116723200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr10:116719200-116724000	Strong transcription	Dnd41	blood
37	chr10:116719400-116723200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr10:116719400-116723400	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr10:116719400-116723600	Strong transcription	Liver	Liver
40	chr10:116719400-116723800	Strong transcription	Adipose Nuclei	Adipose
41	chr10:116719400-116724600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr10:116719600-116723600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr10:116719800-116723000	Strong transcription	Fetal Thymus	thymus
44	chr10:116720000-116723000	Strong transcription	Fetal Intestine Large	intestine
45	chr10:116720000-116723400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr10:116720000-116724600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr10:116720000-116736400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr10:116720400-116730400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr10:116721000-116729200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr10:116721200-116723000	Weak transcription	HMEC	breast

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