Variant report

Variant	rs692872
Chromosome Location	chr10:96163798-96163799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:96120934..96124258-chr10:96160439..96165957,6	MCF-7	breast:
2	chr10:96121306..96124383-chr10:96159927..96163798,5	MCF-7	breast:
3	chr10:96162891..96164490-chr10:96175616..96177129,2	MCF-7	breast:
4	chr10:96162530..96165019-chr10:96199067..96201077,2	MCF-7	breast:
5	chr10:96160448..96164371-chr10:96304138..96307716,8	MCF-7	breast:
6	chr10:96089068..96091434-chr10:96163469..96165336,2	K562	blood:
7	chr10:96162673..96164608-chr10:96201520..96204137,3	MCF-7	breast:
8	chr10:96162368..96164918-chr10:96174079..96176855,3	K562	blood:
9	chr10:96162267..96164235-chr10:96185502..96188240,3	MCF-7	breast:
10	chr10:96162320..96165263-chr10:96165537..96170524,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000173145	Chromatin interaction
ENSG00000119969	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10786168	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs10786169	1.00[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs1079504	0.83[EUR][1000 genomes]
rs10882452	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10882454	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10882460	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10882463	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10882469	0.88[EUR][1000 genomes]
rs10882470	0.91[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap]
rs10882471	0.89[EUR][1000 genomes]
rs10882473	0.86[EUR][1000 genomes]
rs10882474	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs10882477	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11187937	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11187938	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11187939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11187940	0.92[JPT][hapmap]
rs11187944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11187948	0.91[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11187952	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11187958	0.81[EUR][1000 genomes]
rs11187960	1.00[JPT][hapmap]
rs11187966	0.82[EUR][1000 genomes]
rs11187972	0.95[CEU][hapmap];0.80[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11187973	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11187980	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11187996	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11188009	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs11188012	0.83[JPT][hapmap]
rs11188019	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs11188020	1.00[JPT][hapmap]
rs11188040	0.87[MEX][hapmap]
rs11527881	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11592354	0.90[EUR][1000 genomes]
rs12218213	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs12218216	0.87[MEX][hapmap];0.84[TSI][hapmap]
rs12219906	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs12220588	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs12221475	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12572040	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12762574	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1326839	0.92[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs1334595	1.00[JPT][hapmap]
rs1749352	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1749355	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1749356	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1854035	0.80[EUR][1000 genomes]
rs1886272	0.85[EUR][1000 genomes]
rs1889485	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1889486	0.91[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1931757	0.83[JPT][hapmap]
rs1969815	0.85[CEU][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs1977288	1.00[JPT][hapmap]
rs1977291	0.83[JPT][hapmap]
rs1980741	1.00[CEU][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2095380	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2244241	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2265362	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2265364	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274096	0.82[EUR][1000 genomes]
rs2274417	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs2281791	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2860760	0.82[EUR][1000 genomes]
rs2860821	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs2901764	0.81[EUR][1000 genomes]
rs2901765	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3758523	0.81[EUR][1000 genomes]
rs3781262	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4351744	1.00[CEU][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4611135	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs479664	0.81[EUR][1000 genomes]
rs480032	1.00[JPT][hapmap]
rs4917505	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4918333	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4918402	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs4918404	0.82[EUR][1000 genomes]
rs4918409	0.85[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs4918419	0.85[CEU][hapmap]
rs493088	0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs517784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs522111	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs541704	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs542540	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs555782	0.83[EUR][1000 genomes]
rs556055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56020662	0.82[EUR][1000 genomes]
rs576517	0.84[EUR][1000 genomes]
rs581165	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6583942	1.00[JPT][hapmap]
rs6583943	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6583944	0.85[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs6583946	0.81[EUR][1000 genomes]
rs7073639	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7078236	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7078478	0.83[JPT][hapmap]
rs7078811	1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs7079934	0.83[EUR][1000 genomes]
rs7083898	1.00[CEU][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7086462	0.81[EUR][1000 genomes]
rs7087798	0.83[JPT][hapmap]
rs7089094	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7092129	1.00[JPT][hapmap]
rs7895305	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7898330	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7906843	0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs7913343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7921721	1.00[CEU][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8181426	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs912466	0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs9420641	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs945123	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs955694	0.82[EUR][1000 genomes]
rs9633675	0.80[ASN][1000 genomes]
rs9633699	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761616	chr10:95966768-96303701	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv831946	chr10:96055190-96226438	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1819509	chr10:96064300-96361776	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	esv3398177	chr10:96139011-96169931	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3411992	chr10:96139011-96172041	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	esv3359689	chr10:96161587-96164135	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	esv3372349	chr10:96161987-96164835	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	esv1801044	chr10:96162545-96170593	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	esv1815355	chr10:96162545-96189900	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	esv1817623	chr10:96162545-96189900	Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs692872	C19orf22	trans	cerebellum	SCAN
rs692872	FGFBP3	cis	cerebellum	SCAN
rs692872	HELLS	cis	cerebellum	SCAN
rs692872	KIF11	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96161200-96164000	Active TSS	Placenta	Placenta
2	chr10:96161600-96163800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr10:96161600-96164200	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr10:96161600-96164600	Active TSS	Rectal Smooth Muscle	rectum
5	chr10:96161600-96164800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr10:96161600-96164800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr10:96161600-96164800	Active TSS	Stomach Smooth Muscle	stomach
8	chr10:96161600-96164800	Active TSS	Hela-S3	cervix
9	chr10:96161600-96165000	Active TSS	Brain Anterior Caudate	brain
10	chr10:96161600-96165000	Active TSS	Fetal Intestine Large	intestine
11	chr10:96161600-96165400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr10:96161800-96163800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr10:96161800-96163800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr10:96161800-96163800	Active TSS	Esophagus	oesophagus
15	chr10:96161800-96163800	Active TSS	Fetal Kidney	kidney
16	chr10:96161800-96163800	Active TSS	Gastric	stomach
17	chr10:96161800-96164000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr10:96161800-96164000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
19	chr10:96161800-96164000	Active TSS	Fetal Muscle Trunk	muscle
20	chr10:96161800-96164000	Active TSS	Fetal Stomach	stomach
21	chr10:96161800-96164000	Active TSS	Left Ventricle	heart
22	chr10:96161800-96164000	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr10:96161800-96164000	Bivalent/Poised TSS	Thymus	Thymus
24	chr10:96161800-96164000	Active TSS	HUVEC	blood vessel
25	chr10:96161800-96164200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr10:96161800-96164200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr10:96161800-96164200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr10:96161800-96164200	Active TSS	Colon Smooth Muscle	Colon
29	chr10:96161800-96164200	Active TSS	Ovary	ovary
30	chr10:96161800-96164200	Active TSS	Psoas Muscle	Psoas
31	chr10:96161800-96164200	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr10:96161800-96164400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr10:96161800-96164400	Active TSS	Fetal Lung	lung
34	chr10:96161800-96164600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:96161800-96164600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr10:96161800-96164600	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr10:96161800-96164800	Active TSS	Aorta	Aorta
38	chr10:96161800-96164800	Active TSS	Colonic Mucosa	Colon
39	chr10:96161800-96164800	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr10:96161800-96164800	Active TSS	Pancreas	Pancrea
41	chr10:96161800-96164800	Active TSS	Right Atrium	heart
42	chr10:96161800-96165000	Active TSS	Brain Hippocampus Middle	brain
43	chr10:96161800-96165000	Active TSS	HMEC	breast
44	chr10:96161800-96165200	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr10:96161800-96165200	Active TSS	Brain Cingulate Gyrus	brain
46	chr10:96161800-96165200	Active TSS	GM12878-XiMat	blood
47	chr10:96161800-96165200	Active TSS	Osteobl	bone
48	chr10:96161800-96165400	Active TSS	Brain Angular Gyrus	brain
49	chr10:96161800-96165400	Active TSS	Duodenum Mucosa	Duodenum
50	chr10:96161800-96165400	Active TSS	NHLF	lung

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