Variant report

Variant	rs6494065
Chromosome Location	chr15:59345448-59345449
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	TCF12	chr15:59345047-59345559	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr15:59344993-59345637	SK-N-SH	brain:	n/a	n/a
3	CEBPB	chr15:59345321-59345560	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59344021..59346985-chr15:59348905..59351426,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241640	TF binding region

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10431791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10431792	0.86[ASN][1000 genomes]
rs10518996	0.92[ASW][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs1074701	0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10851643	0.95[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs11071405	0.85[ASN][1000 genomes]
rs11635820	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11852461	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11855536	0.86[CEU][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs12050865	0.83[ASN][1000 genomes]
rs12101733	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12437587	0.86[ASN][1000 genomes]
rs12438111	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12438128	0.81[ASN][1000 genomes]
rs12438208	0.86[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs12438962	0.85[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap]
rs12440692	0.81[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12441973	0.85[ASN][1000 genomes]
rs12442086	0.81[JPT][hapmap]
rs12900369	0.82[ASN][1000 genomes]
rs12902628	0.82[ASN][1000 genomes]
rs12906212	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs12907187	0.82[ASN][1000 genomes]
rs12913177	0.81[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12915899	0.90[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap]
rs1345116	0.95[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs1374155	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs1374156	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1446237	0.91[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1446238	0.94[CEU][hapmap];0.83[CHB][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1446239	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1665049	0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1665050	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1665051	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1693532	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs16940998	0.91[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.80[MEX][hapmap]
rs17236369	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17236383	0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs17302142	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17302163	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17302191	0.84[CEU][hapmap];0.85[JPT][hapmap]
rs1867757	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs1968606	0.83[ASN][1000 genomes]
rs1968607	0.83[ASN][1000 genomes]
rs1975534	0.84[ASN][1000 genomes]
rs2084161	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap]
rs2121236	0.81[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2121237	0.82[ASN][1000 genomes]
rs2289895	0.85[CHD][hapmap];0.91[GIH][hapmap]
rs2414618	0.83[ASN][1000 genomes]
rs2414619	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28391430	0.82[ASN][1000 genomes]
rs28514475	0.82[ASN][1000 genomes]
rs28610479	0.82[ASN][1000 genomes]
rs2899640	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs34338282	0.82[ASN][1000 genomes]
rs34718679	0.90[ASN][1000 genomes]
rs34977427	0.86[ASN][1000 genomes]
rs35066133	0.86[ASN][1000 genomes]
rs35204615	0.82[ASN][1000 genomes]
rs35210199	0.81[ASN][1000 genomes]
rs35460138	0.81[ASN][1000 genomes]
rs35555888	0.82[ASN][1000 genomes]
rs35658945	0.81[ASN][1000 genomes]
rs4218	0.86[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap]
rs4531679	0.92[ASW][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs4774320	0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs4774321	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4775110	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs4775111	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4775114	0.83[ASN][1000 genomes]
rs57557135	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58335303	0.89[ASN][1000 genomes]
rs58417366	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59540276	0.82[ASN][1000 genomes]
rs61022867	0.82[ASN][1000 genomes]
rs62002516	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6494054	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6494064	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6494069	0.92[ASW][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs7165028	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7168102	0.93[ASN][1000 genomes]
rs7173135	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7175215	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7175246	0.90[ASN][1000 genomes]
rs7175490	0.81[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs7176281	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7176576	0.90[ASN][1000 genomes]
rs7178935	1.00[ASW][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs73418863	0.81[ASN][1000 genomes]
rs73418864	0.82[ASN][1000 genomes]
rs8025246	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8026611	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8027536	0.94[ASN][1000 genomes]
rs8028752	0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs8028764	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap];0.90[ASN][1000 genomes]
rs8029336	0.86[ASN][1000 genomes]
rs8030246	0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs8030323	0.87[ASN][1000 genomes]
rs8031390	0.87[ASN][1000 genomes]
rs8037569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8039514	0.91[CEU][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes]
rs8040456	0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs8041221	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8041704	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8042516	0.81[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs8042896	0.82[ASN][1000 genomes]
rs877269	0.82[JPT][hapmap]
rs9302206	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9788719	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
3	esv1850946	chr15:59174539-59429160	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats 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	70 gene(s)	inside rSNPs	diseases
4	nsv904271	chr15:59249584-59393011	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv520679	chr15:59268410-59376531	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv520872	chr15:59268410-59395184	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv510663	chr15:59310676-59370041	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
8	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6494065	NARG2	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59281200-59352600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:59281400-59347800	Weak transcription	Colonic Mucosa	Colon
3	chr15:59281800-59352200	Weak transcription	Aorta	Aorta
4	chr15:59281800-59353400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:59283800-59359000	Weak transcription	Fetal Brain Male	brain
6	chr15:59288400-59351200	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:59295200-59349200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr15:59305400-59354400	Weak transcription	Gastric	stomach
9	chr15:59306000-59353400	Weak transcription	Fetal Heart	heart
10	chr15:59308400-59358000	Weak transcription	Spleen	Spleen
11	chr15:59309200-59359000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:59323600-59359000	Weak transcription	Esophagus	oesophagus
13	chr15:59323800-59347600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:59323800-59348400	Weak transcription	Brain Anterior Caudate	brain
15	chr15:59324000-59347800	Weak transcription	NHLF	lung
16	chr15:59324000-59350600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr15:59324000-59350600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr15:59324000-59351000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:59325000-59354800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:59325200-59345800	Weak transcription	NHDF-Ad	bronchial
21	chr15:59325400-59347800	Weak transcription	HSMMtube	muscle
22	chr15:59325400-59350000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:59325400-59352000	Weak transcription	Fetal Lung	lung
24	chr15:59325800-59345800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:59325800-59348800	Weak transcription	Fetal Kidney	kidney
26	chr15:59325800-59350600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr15:59326400-59349400	Weak transcription	Colon Smooth Muscle	Colon
28	chr15:59326400-59365200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr15:59327600-59347800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr15:59328400-59348000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:59328800-59350600	Weak transcription	Brain Germinal Matrix	brain
32	chr15:59329000-59350800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr15:59329200-59349000	Weak transcription	NHEK	skin
34	chr15:59329200-59352200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:59329200-59352600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:59329400-59352600	Weak transcription	Pancreas	Pancrea
37	chr15:59329600-59346600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:59331000-59351600	Weak transcription	Fetal Brain Female	brain
39	chr15:59332400-59350600	Weak transcription	Thymus	Thymus
40	chr15:59332400-59358200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr15:59335800-59350600	Weak transcription	Lung	lung
42	chr15:59335800-59354400	Weak transcription	Psoas Muscle	Psoas
43	chr15:59336000-59345600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:59336000-59349000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:59336800-59347400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:59339600-59345800	Weak transcription	Fetal Intestine Large	intestine
47	chr15:59339800-59352600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr15:59340000-59346000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:59340000-59350000	Weak transcription	Fetal Muscle Leg	muscle
50	chr15:59340000-59352600	Weak transcription	Ovary	ovary

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