Variant report

Variant	rs957603
Chromosome Location	chr15:41009668-41009669
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	chr15:41008193..41010790-chr15:41016125..41018325,2	K562	blood:
2	chr15:41001672..41003745-chr15:41008765..41011053,2	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10152546	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1044474	0.89[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs10518697	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1058734	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11070283	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12148915	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12385982	0.82[AMR][1000 genomes]
rs12442560	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591044	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903817	0.92[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12907442	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12908316	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12913739	0.92[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs12915171	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12915636	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17673703	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs17674454	0.92[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs17747423	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17747633	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1801321	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2619682	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28529389	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs28866515	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28891195	0.86[AMR][1000 genomes]
rs34305357	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34739056	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35127391	0.84[AMR][1000 genomes]
rs35684277	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4923880	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4924486	0.92[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4924492	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924498	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4924502	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5030789	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56409425	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59244061	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492964	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71471880	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7165509	0.92[CEU][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7175747	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7175905	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7176245	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7176590	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7177265	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180135	1.00[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]
rs7182499	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029530	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8036891	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8037180	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8038122	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8042386	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9920676	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	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
6	nsv527234	chr15:40987725-41031686	Transcr. at gene 5' and 3' Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs957603	C15orf57	cis	Esophagus Muscularis	GTEx
rs957603	C15orf57	cis	lung	GTEx
rs957603	MAPKBP1	cis	cerebellum	SCAN
rs957603	CCDC32	cis	multi-tissue	Pritchard
rs957603	SPINT1	cis	multi-tissue	Pritchard
rs957603	MRPL42P5	cis	multi-tissue	Pritchard
rs957603	RP11-111A22.1	cis	Artery Tibial	GTEx
rs957603	C15orf57	cis	Esophagus Mucosa	GTEx
rs957603	C15orf57	cis	Stomach	GTEx
rs957603	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs957603	C15orf57	cis	Nerve Tibial	GTEx
rs957603	C15orf57	cis	Adipose Subcutaneous	GTEx
rs957603	RAD51	cis	multi-tissue	Pritchard
rs957603	RP11-111A22.1	cis	lung	GTEx
rs957603	CCDC32	cis	normal skin	skin_eQTL
rs957603	MRPL42P5	cis	lymphoblastoid	seeQTL
rs957603	C15orf57	cis	Muscle Skeletal	GTEx
rs957603	C15orf57	cis	Artery Aorta	GTEx
rs957603	C15orf57	cis	Heart Left Ventricle	GTEx
rs957603	C15orf57	cis	Artery Tibial	GTEx
rs957603	C15orf57	cis	parietal	SCAN
rs957603	C15orf57	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40988000-41030000	Weak transcription	Pancreas	Pancrea
2	chr15:40988200-41028600	Weak transcription	Spleen	Spleen
3	chr15:40988400-41020600	Weak transcription	Placenta	Placenta
4	chr15:40988400-41020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:40988400-41021600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:40988400-41021800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:40988400-41027200	Weak transcription	Primary B cells from cord blood	blood
8	chr15:40988400-41031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:40988600-41018400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:40988600-41021400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:40988600-41021400	Weak transcription	Fetal Brain Female	brain
12	chr15:40988800-41020600	Weak transcription	Primary T cells from cord blood	blood
13	chr15:40988800-41021600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:40988800-41021800	Weak transcription	Fetal Kidney	kidney
15	chr15:40989000-41012000	Weak transcription	NHLF	lung
16	chr15:40989000-41018000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:40990200-41013200	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr15:40990200-41016800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:40990200-41016800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:40990600-41015000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:40990600-41022600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:40990800-41016000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:40992000-41016600	Strong transcription	Dnd41	blood
24	chr15:40993200-41025800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr15:40994000-41020600	Weak transcription	HSMM	muscle
26	chr15:40997800-41020800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr15:40998200-41023200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:40998800-41038000	Weak transcription	Stomach Mucosa	stomach
29	chr15:40999000-41011600	Weak transcription	Fetal Intestine Large	intestine
30	chr15:40999000-41027600	Weak transcription	Gastric	stomach
31	chr15:40999200-41021600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:41000000-41026000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr15:41001400-41020800	Weak transcription	NHDF-Ad	bronchial
34	chr15:41001600-41020600	Weak transcription	NH-A	brain
35	chr15:41002000-41019600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:41002000-41021400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:41002200-41011000	Weak transcription	Fetal Intestine Small	intestine
38	chr15:41002200-41021600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr15:41002800-41019400	Weak transcription	Fetal Stomach	stomach
40	chr15:41003200-41021800	Weak transcription	Brain Germinal Matrix	brain
41	chr15:41003400-41010200	Weak transcription	Thymus	Thymus
42	chr15:41003600-41010800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr15:41003600-41013800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:41003600-41021800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr15:41003800-41015600	Weak transcription	HMEC	breast
46	chr15:41003800-41023800	Weak transcription	Fetal Lung	lung
47	chr15:41004000-41021600	Weak transcription	Osteobl	bone
48	chr15:41004600-41021000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr15:41004800-41010800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:41004800-41012600	Weak transcription	NHEK	skin

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