Variant report

Variant	rs316604
Chromosome Location	chr15:41775221-41775222
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41773035..41782898-chr15:41783132..41789747,15	K562	blood:
2	chr15:41768098..41770012-chr15:41773199..41776033,2	K562	blood:
3	chr15:41768645..41771013-chr15:41774949..41776916,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137815	Chromatin interaction
ENSG00000137825	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10518717	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs11070328	1.00[ASW][hapmap];0.93[CEU][hapmap];0.92[GIH][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs11629979	1.00[ASN][1000 genomes]
rs11630656	1.00[ASN][1000 genomes]
rs11630799	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635269	1.00[ASN][1000 genomes]
rs11635565	1.00[ASN][1000 genomes]
rs11635906	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854081	0.93[CEU][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs11854632	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];0.94[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854820	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858068	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858812	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13313520	0.91[ASW][hapmap];0.93[CEU][hapmap];0.92[GIH][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs13380007	0.88[YRI][hapmap]
rs1617832	0.85[LWK][hapmap];0.81[YRI][hapmap]
rs1757468	0.93[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730589	0.91[ASW][hapmap];0.87[CEU][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs17730888	1.00[ASW][hapmap];0.93[CEU][hapmap];0.88[GIH][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs1866399	1.00[ASN][1000 genomes]
rs1899	1.00[ASW][hapmap];0.93[CEU][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118740	0.81[CEU][hapmap];1.00[ASN][1000 genomes]
rs2730056	0.93[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730058	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28377562	1.00[ASN][1000 genomes]
rs28416360	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28421136	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437576	1.00[ASN][1000 genomes]
rs28456082	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28458941	1.00[ASN][1000 genomes]
rs28459164	0.84[EUR][1000 genomes]
rs28463309	1.00[ASW][hapmap];0.93[CEU][hapmap];0.92[GIH][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs28477406	1.00[ASN][1000 genomes]
rs28492932	1.00[ASN][1000 genomes]
rs28493702	1.00[ASN][1000 genomes]
rs28535540	1.00[ASN][1000 genomes]
rs28555198	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557159	0.87[CEU][hapmap];1.00[ASN][1000 genomes]
rs28576457	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28584379	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28617619	1.00[ASN][1000 genomes]
rs28623183	1.00[ASN][1000 genomes]
rs28661013	1.00[ASN][1000 genomes]
rs28663426	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28673484	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28687846	1.00[ASN][1000 genomes]
rs28700583	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28703570	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28712264	1.00[ASN][1000 genomes]
rs28716689	1.00[ASN][1000 genomes]
rs28897479	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316606	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316607	0.93[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316611	0.86[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316616	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316618	0.81[YRI][hapmap]
rs3204853	0.93[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34040639	0.93[CEU][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34285452	0.82[EUR][1000 genomes]
rs34665396	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55725658	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56400990	1.00[ASN][1000 genomes]
rs59000092	1.00[ASN][1000 genomes]
rs6493000	1.00[ASN][1000 genomes]
rs6493003	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162231	1.00[ASN][1000 genomes]
rs7163989	1.00[ASN][1000 genomes]
rs7164211	0.91[ASW][hapmap];0.93[CEU][hapmap];0.96[GIH][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.94[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164684	0.93[CEU][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165396	1.00[ASN][1000 genomes]
rs7165914	0.91[ASW][hapmap];0.93[CEU][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs7167706	1.00[ASN][1000 genomes]
rs7168002	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168307	0.87[CEU][hapmap];1.00[ASN][1000 genomes]
rs7168431	0.93[CEU][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169543	0.91[ASW][hapmap];0.93[CEU][hapmap];0.92[GIH][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs7181982	0.93[CEU][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs7182324	1.00[ASN][1000 genomes]
rs72739630	1.00[ASN][1000 genomes]
rs72739644	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023530	0.87[CEU][hapmap];1.00[ASN][1000 genomes]
rs8034840	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036026	0.93[CEU][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs8036734	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037574	0.87[CEU][hapmap];1.00[ASN][1000 genomes]
rs8038132	1.00[ASN][1000 genomes]
rs8041809	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs316604	KRTAP4-7	cis	lesional skin	skin_eQTL
rs316604	KRTAP4-7	cis	normal skin	skin_eQTL
rs316604	OIP5-AS1	cis	Nerve Tibial	GTEx
rs316604	NDUFAF1	cis	cerebellum	SCAN
rs316604	NDUFAF1	cis	lung	GTEx
rs316604	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs316604	GPR176	cis	parietal	SCAN
rs316604	RPAP1	cis	parietal	SCAN
rs316604	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs316604	NDUFAF1	cis	Muscle Skeletal	GTEx
rs316604	NUSAP1	cis	parietal	SCAN
rs316604	NDUFAF1	cis	multi-tissue	Pritchard
rs316604	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs316604	NUSAP1	cis	cerebellum	SCAN
rs316604	SPINT1	cis	cerebellum	SCAN
rs316604	ZFP106	cis	parietal	SCAN
rs316604	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs316604	OIP5-AS1	cis	Artery Tibial	GTEx
rs316604	RASGRP1	cis	cerebellum	SCAN
rs316604	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs316604	NDUFAF1	cis	parietal	SCAN
rs316604	KRTAP4-7	cis	uninvolved skin	skin_eQTL
rs316604	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs316604	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs316604	NDUFAF1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41724200-41777200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:41745200-41775800	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:41753800-41776800	Strong transcription	Fetal Muscle Leg	muscle
4	chr15:41754200-41776000	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr15:41754400-41776800	Strong transcription	Placenta	Placenta
6	chr15:41755000-41775600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr15:41756800-41776200	Strong transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:41757000-41776200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:41757000-41776400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:41757200-41775400	Strong transcription	Fetal Thymus	thymus
11	chr15:41757400-41776800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr15:41760800-41775600	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr15:41761000-41776400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:41762000-41776000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:41764600-41775800	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr15:41764800-41776000	Strong transcription	Fetal Lung	lung
17	chr15:41765000-41777200	Strong transcription	Stomach Smooth Muscle	stomach
18	chr15:41765200-41775400	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr15:41765400-41775400	Strong transcription	Adipose Nuclei	Adipose
20	chr15:41765600-41775400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:41765600-41775600	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:41765600-41775600	Strong transcription	Brain Hippocampus Middle	brain
23	chr15:41765600-41775800	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:41765600-41775800	Strong transcription	Brain Anterior Caudate	brain
25	chr15:41765600-41775800	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr15:41765600-41776000	Strong transcription	Brain Substantia Nigra	brain
27	chr15:41765600-41776800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:41765600-41778400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:41765800-41775400	Strong transcription	HSMMtube	muscle
30	chr15:41766600-41776000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:41766600-41776400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:41767600-41775400	Strong transcription	Liver	Liver
33	chr15:41767600-41776200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:41767600-41776600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:41769400-41775600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:41769600-41776000	Strong transcription	Left Ventricle	heart
37	chr15:41769600-41776000	Strong transcription	HSMM	muscle
38	chr15:41769600-41779200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:41769600-41780200	Weak transcription	Right Atrium	heart
40	chr15:41769800-41776200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:41770000-41776000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:41770000-41776000	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr15:41770000-41776800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:41770200-41775400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr15:41770200-41776000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:41770200-41776800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr15:41770200-41777000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:41770600-41777200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:41770800-41775600	Strong transcription	Brain Angular Gyrus	brain
50	chr15:41770800-41776200	Strong transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links