Variant report

Variant	rs4924503
Chromosome Location	chr15:41045329-41045330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41044630..41047663-chr15:41185217..41189065,4	K562	blood:
2	chr15:41042059..41049706-chr15:41053861..41061949,15	MCF-7	breast:
3	chr15:40987359..40990886-chr15:41044779..41048321,5	K562	blood:
4	chr15:41045121..41047501-chr15:41186359..41188842,2	K562	blood:
5	chr15:40984748..40990654-chr15:41044779..41050104,8	K562	blood:

Variant related genes	Relation type
ENSG00000245849	Chromatin interaction
ENSG00000051180	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000137880	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10775121	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070293	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631563	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11633269	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11852786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11855560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11858337	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11858338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12372947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439683	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12441514	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12442845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12593359	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12908284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12912742	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2263551	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2412546	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412547	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412548	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412549	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2577564	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2619679	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2619680	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2619683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2917955	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2928140	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3092982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3092983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3101861	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34400306	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36106105	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs45495293	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4923884	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924493	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924495	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56042757	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492961	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7164339	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7167854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169010	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7172195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7173646	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7174551	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7175401	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs752012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025883	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8033829	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8036817	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4924503	RP11-111A22.1	cis	Artery Tibial	GTEx
rs4924503	C15orf57	cis	Artery Tibial	GTEx
rs4924503	RP11-111A22.1	cis	lung	GTEx
rs4924503	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs4924503	C15orf57	cis	Adipose Subcutaneous	GTEx
rs4924503	CCDC32	cis	multi-tissue	Pritchard
rs4924503	C15orf57	cis	lung	GTEx
rs4924503	C15orf57	cis	Nerve Tibial	GTEx
rs4924503	RAD51	cis	multi-tissue	Pritchard
rs4924503	CCDC32	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41008200-41046600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:41019400-41046200	Strong transcription	Fetal Stomach	stomach
3	chr15:41020800-41045400	Strong transcription	Fetal Muscle Trunk	muscle
4	chr15:41025600-41045400	Strong transcription	Stomach Smooth Muscle	stomach
5	chr15:41031000-41046600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:41032600-41046200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:41032600-41046600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:41032600-41046600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr15:41034200-41045800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr15:41034600-41045800	Genic enhancers	Fetal Intestine Small	intestine
11	chr15:41034800-41046200	Genic enhancers	Fetal Intestine Large	intestine
12	chr15:41035800-41046600	Weak transcription	Right Atrium	heart
13	chr15:41036600-41045400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:41036600-41045800	Weak transcription	NH-A	brain
15	chr15:41036800-41046000	Weak transcription	Fetal Heart	heart
16	chr15:41036800-41046200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:41037000-41045600	Strong transcription	NHEK	skin
18	chr15:41037200-41046200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:41037400-41045800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr15:41038200-41046600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:41039400-41045400	Strong transcription	Brain Anterior Caudate	brain
22	chr15:41039800-41046600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:41040800-41045600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr15:41042800-41045400	Strong transcription	Osteobl	bone
25	chr15:41043000-41046200	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr15:41043200-41045400	Genic enhancers	Duodenum Mucosa	Duodenum
27	chr15:41043400-41046600	Weak transcription	Fetal Kidney	kidney
28	chr15:41043400-41046600	Weak transcription	Stomach Mucosa	stomach
29	chr15:41043600-41046600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:41043800-41046400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr15:41044000-41046200	Weak transcription	HSMM	muscle
32	chr15:41044000-41046200	Transcr. at gene 5' and 3'	K562	blood
33	chr15:41044000-41046600	Weak transcription	NHDF-Ad	bronchial
34	chr15:41044200-41045400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:41044200-41045800	Weak transcription	HMEC	breast
36	chr15:41044200-41046200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr15:41044200-41046600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:41044400-41045400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
39	chr15:41044400-41045400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
40	chr15:41044400-41045800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:41044400-41045800	Weak transcription	Esophagus	oesophagus
42	chr15:41044400-41045800	Weak transcription	HUVEC	blood vessel
43	chr15:41044400-41045800	Weak transcription	NHLF	lung
44	chr15:41044400-41046000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:41044400-41046000	Weak transcription	A549	lung
46	chr15:41044400-41046400	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr15:41044400-41046400	Weak transcription	Colonic Mucosa	Colon
48	chr15:41044400-41046400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:41044400-41046400	Weak transcription	Left Ventricle	heart
50	chr15:41044400-41046600	Weak transcription	H9 Cell Line	embryonic stem cell

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