Variant report

Variant	rs17015025
Chromosome Location	chr4:90034030-90034031
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	MBD4	chr4:90033300-90034049	HepG2	liver:	n/a	n/a
2	ARID3A	chr4:90032770-90035534	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:90032368-90036875	HepG2	liver:	n/a	n/a
4	MXI1	chr4:90031723-90034038	HepG2	liver:	n/a	chr4:90031789-90031804
5	POLR2A	chr4:90032398-90034599	HepG2	liver:	n/a	n/a
6	POLR2A	chr4:90032629-90036890	K562	blood:	n/a	n/a
7	POLR2A	chr4:90031723-90036966	HepG2	liver:	n/a	n/a
8	MAZ	chr4:90031671-90034255	IMR90	lung:	n/a	chr4:90032609-90032618 chr4:90032634-90032644
9	POLR2A	chr4:90033559-90034087	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:90032059-90034809	GM12878	blood:	n/a	n/a
11	POLR2A	chr4:90034019-90034311	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
FAM13A	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10025332	0.83[ASN][1000 genomes]
rs10516826	0.92[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10516828	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12507349	0.89[ASN][1000 genomes]
rs1343921	0.88[JPT][hapmap]
rs1398945	0.89[ASN][1000 genomes]
rs1513820	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17768752	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17769356	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17770293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17819929	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17820320	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17821105	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1795731	0.93[GIH][hapmap]
rs1921680	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2175821	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2280099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670625	0.82[CHD][hapmap];0.93[GIH][hapmap]
rs2869974	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3822085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5026462	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55806245	0.84[ASN][1000 genomes]
rs55885459	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55987745	0.87[ASN][1000 genomes]
rs55996516	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56038841	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56111951	0.89[ASN][1000 genomes]
rs56147277	0.84[ASN][1000 genomes]
rs56165603	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56344658	0.89[ASN][1000 genomes]
rs56355329	0.89[ASN][1000 genomes]
rs56672432	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56719325	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59188553	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59283403	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59586695	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60213126	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60591238	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60751124	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61082288	0.84[ASN][1000 genomes]
rs62306393	0.98[ASN][1000 genomes]
rs6822256	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6825767	0.83[ASN][1000 genomes]
rs6825804	0.83[ASN][1000 genomes]
rs6826703	0.81[ASN][1000 genomes]
rs6832298	0.84[ASN][1000 genomes]
rs72665855	0.81[ASN][1000 genomes]
rs72665867	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72665868	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72665882	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72665892	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72665898	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72665902	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72668111	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668112	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668120	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668125	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72668127	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72668130	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72668134	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72668135	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72668138	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72668144	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72668152	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668154	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668156	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668157	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668165	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668167	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668171	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668179	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72668183	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668187	0.89[ASN][1000 genomes]
rs72668189	0.87[ASN][1000 genomes]
rs72668192	0.84[ASN][1000 genomes]
rs72668193	0.84[ASN][1000 genomes]
rs72668195	0.83[ASN][1000 genomes]
rs72668196	0.83[ASN][1000 genomes]
rs72670003	0.83[ASN][1000 genomes]
rs7440590	0.82[CHD][hapmap]
rs756227	0.83[ASN][1000 genomes]
rs7660709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7669140	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7689498	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7691983	0.82[CHD][hapmap]
rs8582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993181	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3437234	chr4:90031454-90034302	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17015025	KLK7	trans	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90032400-90034400	Active TSS	Placenta	Placenta
2	chr4:90033000-90034200	Flanking Active TSS	HMEC	breast
3	chr4:90033200-90034200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:90033200-90034200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:90033400-90034200	Flanking Active TSS	Liver	Liver
6	chr4:90033400-90048200	Weak transcription	Ovary	ovary
7	chr4:90033400-90049200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:90033600-90034200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:90033600-90034200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr4:90033600-90034200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:90033600-90034200	Flanking Active TSS	Fetal Intestine Small	intestine
12	chr4:90033600-90034200	Enhancers	Placenta Amnion	Placenta Amnion
13	chr4:90033600-90034400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:90033600-90036400	Weak transcription	HUVEC	blood vessel
15	chr4:90033600-90038400	Weak transcription	Psoas Muscle	Psoas
16	chr4:90033600-90039000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:90033600-90039000	Weak transcription	Lung	lung
18	chr4:90033600-90040800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:90033600-90043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:90033600-90045600	Weak transcription	Esophagus	oesophagus
21	chr4:90033600-90045600	Weak transcription	Pancreas	Pancrea
22	chr4:90033600-90049200	Weak transcription	Gastric	stomach
23	chr4:90033600-90052200	Weak transcription	Aorta	Aorta
24	chr4:90033800-90034200	Enhancers	Fetal Brain Male	brain
25	chr4:90033800-90034200	Enhancers	Fetal Heart	heart
26	chr4:90033800-90034200	Enhancers	Hela-S3	cervix
27	chr4:90033800-90034400	Flanking Active TSS	HepG2	liver
28	chr4:90033800-90034600	Weak transcription	Primary T cells from cord blood	blood
29	chr4:90033800-90034600	Transcr. at gene 5' and 3'	A549	lung
30	chr4:90033800-90034800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr4:90033800-90034800	Weak transcription	Fetal Stomach	stomach
32	chr4:90033800-90035000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:90033800-90036200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr4:90033800-90037600	Weak transcription	Fetal Thymus	thymus
35	chr4:90033800-90037600	Weak transcription	HSMM	muscle
36	chr4:90033800-90042400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr4:90034000-90034200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr4:90034000-90034200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
39	chr4:90034000-90034200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:90034000-90034200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:90034000-90034200	Enhancers	Duodenum Mucosa	Duodenum
42	chr4:90034000-90034200	Enhancers	GM12878-XiMat	blood
43	chr4:90034000-90034200	Genic enhancers	K562	blood
44	chr4:90034000-90034200	Enhancers	NHDF-Ad	bronchial
45	chr4:90034000-90034400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:90034000-90034400	Enhancers	Brain Substantia Nigra	brain
47	chr4:90034000-90034400	Weak transcription	Fetal Muscle Leg	muscle
48	chr4:90034000-90034400	Enhancers	Dnd41	blood
49	chr4:90034000-90034600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:90034000-90034600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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