Variant report

Variant	rs7494968
Chromosome Location	chr15:40811858-40811859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40803911..40804534-chr15:40811594..40812575,2	K562	blood:
2	chr15:40628661..40629604-chr15:40811567..40812516,2	K562	blood:
3	chr15:40811763..40813776-chr15:40823296..40825931,2	K562	blood:
4	chr15:40732916..40733625-chr15:40811655..40812334,2	MCF-7	breast:
5	chr15:40811628..40812316-chr15:40881605..40882215,2	MCF-7	breast:
6	chr15:40811570..40813776-chr15:40823296..40826811,3	K562	blood:

Variant related genes	Relation type
ENSG00000140320	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1037445	0.83[EUR][1000 genomes]
rs10400890	0.81[EUR][1000 genomes]
rs10467972	0.83[CHB][hapmap]
rs11070275	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11070277	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070285	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11070286	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11632061	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11632370	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11638742	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11639464	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11852670	0.80[EUR][1000 genomes]
rs11852694	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs11852828	0.80[EUR][1000 genomes]
rs11854986	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs11855334	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11855923	0.96[CEU][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs11856438	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs11856802	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs11858113	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs12594548	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12595610	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12905162	0.96[CEU][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs12914743	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap]
rs12916042	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16970851	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1806961	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1811513	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1813898	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1869301	1.00[CEU][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1869302	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1967368	0.82[EUR][1000 genomes]
rs1993212	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2034651	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2034652	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2167795	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2278888	0.83[CHB][hapmap]
rs2412531	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412532	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412534	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412544	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2444302	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2924386	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2924387	0.83[EUR][1000 genomes]
rs2924388	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2959536	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2959545	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3092979	0.96[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap]
rs35047458	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs3751653	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4080706	0.81[EUR][1000 genomes]
rs4923875	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4923876	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4924472	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4924478	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4924479	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924480	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924481	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs588686	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs590046	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs603623	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs616937	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs618399	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs619711	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs620198	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6492947	0.92[CEU][hapmap]
rs6492951	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs654317	0.86[EUR][1000 genomes]
rs6582	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71471881	0.82[EUR][1000 genomes]
rs7169621	0.83[EUR][1000 genomes]
rs7178756	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7183273	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8026605	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs8028999	0.83[CHB][hapmap]
rs8029384	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8034326	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8036737	0.81[EUR][1000 genomes]
rs8038407	0.84[EUR][1000 genomes]
rs8041534	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs8042729	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs896795	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9652415	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs976401	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs7494968	RP11-111A22.1	cis	lung	GTEx
rs7494968	C15orf57	cis	Esophagus Muscularis	GTEx
rs7494968	CCDC32	cis	lesional skin	skin_eQTL
rs7494968	C15orf57	cis	Artery Tibial	GTEx
rs7494968	C15orf57	cis	Artery Aorta	GTEx
rs7494968	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs7494968	CCDC32	cis	normal skin	skin_eQTL
rs7494968	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs7494968	C15orf57	cis	Heart Left Ventricle	GTEx
rs7494968	C15orf57	cis	Nerve Tibial	GTEx
rs7494968	C15orf57	cis	Lymphoblastoid	GTEx
rs7494968	CCDC32	cis	multi-tissue	Pritchard
rs7494968	C15orf57	cis	Esophagus Mucosa	GTEx
rs7494968	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs7494968	C15orf57	cis	Cerebellum	GTEx
rs7494968	RP11-111A22.1	cis	Artery Tibial	GTEx
rs7494968	C15orf57	cis	lung	GTEx
rs7494968	C15orf57	cis	Muscle Skeletal	GTEx
rs7494968	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs7494968	C15orf57	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40804400-40812200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:40804400-40812200	Weak transcription	Pancreas	Pancrea
3	chr15:40804400-40821000	Weak transcription	Right Atrium	heart
4	chr15:40805000-40812200	Weak transcription	HMEC	breast
5	chr15:40805200-40812200	Weak transcription	Fetal Stomach	stomach
6	chr15:40805200-40828200	Weak transcription	Placenta	Placenta
7	chr15:40805200-40833000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:40806200-40812200	Weak transcription	K562	blood
9	chr15:40809800-40812000	Weak transcription	Adipose Nuclei	Adipose
10	chr15:40810200-40812000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:40811800-40812000	Weak transcription	Brain Hippocampus Middle	brain

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