Variant report

Variant	rs11197010
Chromosome Location	chr10:116714959-116714960
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116696802..116699955-chr10:116713362..116716908,4	MCF-7	breast:
2	chr10:116708122..116710473-chr10:116713973..116715764,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165832	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10160015	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10444099	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10490908	1.00[JPT][hapmap]
rs10510008	0.86[ASN][1000 genomes]
rs10885631	0.82[ASN][1000 genomes]
rs10885632	0.86[ASN][1000 genomes]
rs10885633	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10885634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885637	1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885638	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885639	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196983	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11196984	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11196989	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11196991	1.00[ASN][1000 genomes]
rs11196996	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11196999	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11197000	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11197005	1.00[ASN][1000 genomes]
rs11197006	0.91[ASN][1000 genomes]
rs11197007	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197011	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197012	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197023	0.95[ASN][1000 genomes]
rs12098332	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12246008	0.95[ASN][1000 genomes]
rs12265048	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12269261	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12761122	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12764662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12772737	0.95[ASN][1000 genomes]
rs12774597	0.95[ASN][1000 genomes]
rs12775180	1.00[JPT][hapmap]
rs12779231	0.95[ASN][1000 genomes]
rs17092542	1.00[JPT][hapmap]
rs17721283	1.00[JPT][hapmap]
rs17721905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17722042	0.95[ASN][1000 genomes]
rs17794346	1.00[JPT][hapmap]
rs17795104	0.95[ASN][1000 genomes]
rs17795212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1966384	1.00[JPT][hapmap]
rs2095379	1.00[ASN][1000 genomes]
rs2105001	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420070	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34170154	0.95[ASN][1000 genomes]
rs34434610	0.95[ASN][1000 genomes]
rs34453431	0.95[ASN][1000 genomes]
rs34461950	0.87[ASN][1000 genomes]
rs35501899	0.95[ASN][1000 genomes]
rs35811923	0.95[ASN][1000 genomes]
rs3931556	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs61869271	0.95[ASN][1000 genomes]
rs61869272	0.95[ASN][1000 genomes]
rs61869274	0.95[ASN][1000 genomes]
rs61869275	0.95[ASN][1000 genomes]
rs6585302	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6585306	1.00[ASN][1000 genomes]
rs6585309	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]
rs6585310	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6585311	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6585313	0.95[ASN][1000 genomes]
rs7071789	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7071812	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072356	1.00[JPT][hapmap]
rs7074729	1.00[JPT][hapmap]
rs7075888	1.00[JPT][hapmap]
rs7079234	0.95[ASN][1000 genomes]
rs7085964	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7086663	0.82[GIH][hapmap]
rs7093282	0.83[ASN][1000 genomes]
rs7093330	0.95[ASN][1000 genomes]
rs7094072	1.00[JPT][hapmap]
rs7097580	0.95[ASN][1000 genomes]
rs7099565	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7099590	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7099779	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7100159	1.00[ASN][1000 genomes]
rs7100894	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72836518	0.95[ASN][1000 genomes]
rs749649	1.00[JPT][hapmap]
rs7895551	1.00[JPT][hapmap]
rs7898249	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7904605	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908069	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908464	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7909566	1.00[JPT][hapmap]
rs7909657	1.00[JPT][hapmap]
rs7917523	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7923295	1.00[JPT][hapmap]
rs881192	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951585	0.83[EUR][1000 genomes]
rs968848	0.95[ASN][1000 genomes]
rs968849	0.95[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11197010	ATRNL1	cis	Muscle Skeletal	GTEx
rs11197010	TRUB1	cis	parietal	SCAN
rs11197010	TRUB1	cis	cerebellum	SCAN
rs11197010	TECTB	cis	cerebellum	SCAN

Chromatin state (count:118 , 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	chr10:116699200-116722400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr10:116699200-116722600	Weak transcription	Aorta	Aorta
5	chr10:116699600-116736400	Weak transcription	NHLF	lung
6	chr10:116699800-116722400	Weak transcription	Fetal Kidney	kidney
7	chr10:116699800-116726200	Weak transcription	K562	blood
8	chr10:116700600-116716000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr10:116700800-116722600	Weak transcription	Fetal Brain Male	brain
10	chr10:116701000-116715000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr10:116701200-116716200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr10:116702400-116715200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr10:116702400-116716000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr10:116703400-116730400	Weak transcription	Pancreas	Pancrea
15	chr10:116703600-116715200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr10:116703600-116716800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr10:116703600-116717000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr10:116703600-116722200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr10:116703600-116722400	Weak transcription	Gastric	stomach
20	chr10:116703600-116722400	Weak transcription	Lung	lung
21	chr10:116703600-116722400	Weak transcription	Spleen	Spleen
22	chr10:116703600-116722600	Weak transcription	Brain Substantia Nigra	brain
23	chr10:116703600-116740800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr10:116703600-116747800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr10:116704000-116722000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr10:116705000-116728000	Weak transcription	Small Intestine	intestine
27	chr10:116705200-116721800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr10:116705400-116717200	Weak transcription	Right Ventricle	heart
29	chr10:116705400-116722200	Weak transcription	Fetal Brain Female	brain
30	chr10:116705400-116735400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr10:116705400-116739400	Weak transcription	Thymus	Thymus
32	chr10:116705600-116715800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr10:116705600-116719200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr10:116705600-116722200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr10:116705600-116722200	Weak transcription	Brain Angular Gyrus	brain
36	chr10:116705600-116722200	Weak transcription	Brain Anterior Caudate	brain
37	chr10:116705600-116722200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr10:116705600-116722200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr10:116705600-116722400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr10:116705600-116722400	Weak transcription	Ovary	ovary
41	chr10:116705600-116722400	Weak transcription	Stomach Smooth Muscle	stomach
42	chr10:116705600-116728000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr10:116705800-116717200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr10:116705800-116720400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr10:116705800-116724600	Weak transcription	Colonic Mucosa	Colon
46	chr10:116705800-116730400	Weak transcription	Placenta	Placenta
47	chr10:116706000-116715800	Weak transcription	NHDF-Ad	bronchial
48	chr10:116706000-116717400	Weak transcription	HMEC	breast
49	chr10:116706000-116721800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr10:116706000-116722400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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