Variant report

Variant	rs6585309
Chromosome Location	chr10:116730337-116730338
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr10:116730235-116730545	H1-hESC	embryonic stem cell:	n/a	chr10:116730380-116730389

Variant related genes	Relation type
RNU6-1121P	TF binding region

Extended variants
information (count: 111 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:101)

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	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10885634	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10885636	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];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];1.00[CHD][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];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11197000	1.00[CHB][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[JPT][hapmap];0.95[ASN][1000 genomes]
rs11197010	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][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]
rs11197029	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12098332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];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	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12764662	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12772737	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	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17722042	1.00[ASN][1000 genomes]
rs17794346	1.00[JPT][hapmap]
rs17795104	1.00[ASN][1000 genomes]
rs17795212	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1966384	1.00[JPT][hapmap]
rs2095379	0.95[ASN][1000 genomes]
rs2105001	0.91[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2420070	0.81[ASN][1000 genomes]
rs34170154	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34434610	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34453431	1.00[ASN][1000 genomes]
rs34461950	0.91[ASN][1000 genomes]
rs35501899	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35811923	1.00[ASN][1000 genomes]
rs3931556	1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs61869271	1.00[ASN][1000 genomes]
rs61869272	1.00[ASN][1000 genomes]
rs61869274	1.00[ASN][1000 genomes]
rs61869275	1.00[ASN][1000 genomes]
rs61869297	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6585302	0.81[ASN][1000 genomes]
rs6585306	0.95[ASN][1000 genomes]
rs6585308	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6585310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6585311	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6585313	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071789	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071812	1.00[CHB][hapmap];1.00[CHD][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	1.00[ASN][1000 genomes]
rs7085964	0.90[ASN][1000 genomes]
rs7086663	0.91[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7087420	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7090904	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7093282	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7093330	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094072	1.00[JPT][hapmap]
rs7097580	1.00[ASN][1000 genomes]
rs7099565	1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7099590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099779	0.95[ASN][1000 genomes]
rs7100026	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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]
rs769119	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7895551	1.00[JPT][hapmap]
rs7898249	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7904605	0.91[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];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	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[ASN][1000 genomes]
rs7923295	1.00[JPT][hapmap]
rs881192	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6585309	TECTB	cis	cerebellum	SCAN
rs6585309	TRUB1	cis	parietal	SCAN
rs6585309	ATRNL1	cis	Muscle Skeletal	GTEx
rs6585309	TRUB1	cis	cerebellum	SCAN
rs6585309	ADRB1	cis	parietal	SCAN
rs6585309	ATRNL1	cis	cerebellum	SCAN

Chromatin state (count:107 , 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	chr10:116703400-116730400	Weak transcription	Pancreas	Pancrea
5	chr10:116703600-116740800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr10:116703600-116747800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr10:116705400-116735400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr10:116705400-116739400	Weak transcription	Thymus	Thymus
9	chr10:116705800-116730400	Weak transcription	Placenta	Placenta
10	chr10:116707000-116744200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr10:116707000-116745600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr10:116708800-116742000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr10:116710800-116741200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr10:116711800-116733000	Weak transcription	Hela-S3	cervix
15	chr10:116712600-116730400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr10:116713800-116734200	Weak transcription	Psoas Muscle	Psoas
17	chr10:116714200-116739400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr10:116716400-116743200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr10:116718000-116737400	Weak transcription	NHDF-Ad	bronchial
20	chr10:116718000-116747600	Weak transcription	Osteobl	bone
21	chr10:116720000-116736400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr10:116720400-116730400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr10:116721400-116732800	Weak transcription	Colon Smooth Muscle	Colon
24	chr10:116722600-116731800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr10:116722800-116734000	Weak transcription	Brain Angular Gyrus	brain
26	chr10:116722800-116744400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr10:116722800-116748000	Weak transcription	Aorta	Aorta
28	chr10:116723000-116730400	Weak transcription	Left Ventricle	heart
29	chr10:116723000-116730400	Weak transcription	Right Ventricle	heart
30	chr10:116723000-116731800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr10:116723000-116732800	Weak transcription	Ovary	ovary
32	chr10:116723000-116733400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr10:116723000-116734000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr10:116723000-116734000	Weak transcription	Fetal Kidney	kidney
35	chr10:116723000-116734800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr10:116723000-116736600	Weak transcription	Fetal Thymus	thymus
37	chr10:116723000-116739200	Weak transcription	Fetal Intestine Small	intestine
38	chr10:116723000-116739800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr10:116723000-116741800	Weak transcription	NHEK	skin
40	chr10:116723000-116742000	Weak transcription	Fetal Intestine Large	intestine
41	chr10:116723000-116742200	Weak transcription	Lung	lung
42	chr10:116723000-116742400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr10:116723000-116743400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr10:116723000-116744000	Weak transcription	Gastric	stomach
45	chr10:116723000-116760800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr10:116723200-116731000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr10:116723200-116731800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr10:116723200-116732800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr10:116723200-116734200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr10:116723200-116742000	Weak transcription	Primary T cells fromperipheralblood	blood

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