Variant report

Variant	rs8041717
Chromosome Location	chr15:31276445-31276446
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31269600..31272390-chr15:31276376..31278340,2	K562	blood:
2	chr15:31272157..31276720-chr15:31281759..31286309,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166912	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10047979	0.82[CEU][hapmap];0.84[YRI][hapmap]
rs10163148	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs1043251	0.82[CEU][hapmap]
rs10519726	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs11070678	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11070718	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs1133642	0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs11638295	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs12437580	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439664	0.85[ASN][1000 genomes]
rs12441318	0.85[CHB][hapmap]
rs12442333	0.82[CHB][hapmap]
rs12443369	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12901022	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs12906480	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12914207	0.87[ASN][1000 genomes]
rs12914438	0.85[ASN][1000 genomes]
rs1404467	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1404468	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs1404469	0.92[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs1404470	0.85[ASN][1000 genomes]
rs1425291	0.85[ASN][1000 genomes]
rs1474381	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1474382	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs1524876	0.92[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs1524877	0.82[CEU][hapmap];0.84[YRI][hapmap]
rs16956341	0.83[CHB][hapmap]
rs16956362	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs16956366	0.83[CHB][hapmap]
rs16956414	0.83[CHB][hapmap];0.87[CHD][hapmap]
rs16956422	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs17815804	0.88[CHD][hapmap]
rs1880499	0.92[CHB][hapmap];0.85[ASN][1000 genomes]
rs2042613	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2113945	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs2113946	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs2140735	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2272218	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272219	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293319	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2293320	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2339048	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28564430	0.82[ASN][1000 genomes]
rs28693590	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2873	0.92[CHB][hapmap]
rs2949568	0.85[TSI][hapmap]
rs2949569	0.92[CHB][hapmap];0.84[CHD][hapmap]
rs2949570	0.92[CHB][hapmap]
rs2949572	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2949573	0.92[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs2949575	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2949576	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2949577	0.92[CHB][hapmap];0.85[ASN][1000 genomes]
rs2949578	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2955778	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs2955781	0.81[CEU][hapmap];0.84[YRI][hapmap]
rs2955783	0.92[CHB][hapmap];0.85[ASN][1000 genomes]
rs2955787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955788	0.82[CEU][hapmap]
rs2955789	0.82[CEU][hapmap]
rs2955790	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs2955791	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2955792	0.82[CEU][hapmap]
rs2955796	0.85[CHB][hapmap]
rs2959039	0.85[CHB][hapmap]
rs2959047	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2959050	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959051	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3743231	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3743233	0.82[ASN][1000 genomes]
rs3784588	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs4344701	0.83[ASN][1000 genomes]
rs4779796	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4779797	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs565	0.82[CEU][hapmap]
rs6493352	0.82[CEU][hapmap]
rs6493358	0.83[CHB][hapmap]
rs71474640	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7161812	1.00[CHB][hapmap]
rs7164530	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164939	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7165798	0.92[CHB][hapmap]
rs7169064	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7170710	0.92[CHB][hapmap];0.85[ASN][1000 genomes]
rs7170772	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7175256	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175951	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176351	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs7178375	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7178533	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7182143	0.92[CHB][hapmap]
rs7183880	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs798101	0.85[CHB][hapmap]
rs8040989	0.92[CHB][hapmap];0.80[ASN][1000 genomes]
rs871312	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs872843	0.83[CHB][hapmap]
rs964925	0.84[CHD][hapmap]
rs9806159	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv525795	chr15:30936285-31324531	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1046874	chr15:31008133-31294654	Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
8	nsv832951	chr15:31131239-31304469	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv1039037	chr15:31140415-31277268	Strong transcription ZNF genes & repeats Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv542309	chr15:31140415-31277268	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
12	nsv903834	chr15:31179534-31293774	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv832952	chr15:31204426-31333998	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
15	nsv1052722	chr15:31261834-31609680	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv542315	chr15:31261834-31609680	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8041717	MTMR10	cis	multi-tissue	Pritchard
rs8041717	RP11-932O9.7	cis	Muscle Skeletal	GTEx
rs8041717	SNORD115-35	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31242000-31282800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:31248800-31283000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:31250200-31282200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr15:31250800-31282400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:31251200-31277200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:31251200-31282400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:31251600-31282200	Weak transcription	Hela-S3	cervix
8	chr15:31252800-31282400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:31254600-31277200	Weak transcription	HSMMtube	muscle
10	chr15:31255200-31276800	Weak transcription	Fetal Brain Female	brain
11	chr15:31255600-31277000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:31255800-31277000	Weak transcription	Fetal Intestine Small	intestine
13	chr15:31255800-31277000	Weak transcription	Fetal Stomach	stomach
14	chr15:31256000-31282400	Weak transcription	Fetal Brain Male	brain
15	chr15:31258200-31277000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:31258200-31277800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:31258400-31277000	Weak transcription	Gastric	stomach
18	chr15:31262200-31282200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr15:31262400-31277200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr15:31262400-31277200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:31265600-31276800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr15:31265600-31277000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr15:31266000-31277000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr15:31266400-31278000	Weak transcription	Colonic Mucosa	Colon
25	chr15:31266600-31277400	Weak transcription	Osteobl	bone
26	chr15:31267600-31277200	Weak transcription	A549	lung
27	chr15:31267800-31277200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:31267800-31277800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:31267800-31282000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:31271200-31276800	Weak transcription	Fetal Heart	heart
31	chr15:31271400-31277000	Weak transcription	Stomach Mucosa	stomach
32	chr15:31271600-31276600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:31272000-31276600	Strong transcription	Fetal Muscle Leg	muscle
34	chr15:31272000-31277000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr15:31272000-31277000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:31272000-31277000	Strong transcription	Fetal Thymus	thymus
37	chr15:31272600-31276800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:31272600-31277000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr15:31272600-31277200	Weak transcription	Esophagus	oesophagus
40	chr15:31272800-31276800	Weak transcription	NHDF-Ad	bronchial
41	chr15:31272800-31277200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:31273000-31276800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr15:31273000-31277000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr15:31273000-31277000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:31273000-31277000	Weak transcription	Pancreas	Pancrea
46	chr15:31273000-31277200	Weak transcription	Aorta	Aorta
47	chr15:31273000-31277200	Strong transcription	Thymus	Thymus
48	chr15:31273000-31279600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr15:31273400-31277200	Weak transcription	Dnd41	blood
50	chr15:31273600-31276800	Strong transcription	Primary T cells from cord blood	blood

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