Variant report

Variant	rs4400148
Chromosome Location	chr5:95988787-95988788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:95982894..95985844-chr5:95986836..95989729,2	MCF-7	breast:
2	chr5:95987202..95990491-chr5:95996534..96000051,5	MCF-7	breast:
3	chr5:95976037..95979831-chr5:95983868..95989174,6	MCF-7	breast:
4	chr5:95987307..95988959-chr5:96004331..96007033,2	K562	blood:
5	chr5:95975136..95978102-chr5:95987198..95988940,2	MCF-7	breast:
6	chr5:95985902..95988959-chr5:96004331..96007887,4	K562	blood:

Variant related genes	Relation type
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10515243	0.82[YRI][hapmap]
rs10866771	0.82[ASN][1000 genomes]
rs11738358	0.82[YRI][hapmap]
rs11739478	0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs11743648	0.83[ASN][1000 genomes]
rs13183352	0.82[ASW][hapmap]
rs13184900	0.85[ASN][1000 genomes]
rs1421912	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152006	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs26486	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs31247	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34847574	0.87[ASN][1000 genomes]
rs35015183	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4434401	0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs4869148	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4869306	0.82[CEU][hapmap]
rs62364719	0.87[ASN][1000 genomes]
rs6891870	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7715982	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7724759	0.82[ASW][hapmap]

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	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4400148	ERAP2	cis	cerebellum	SCAN
rs4400148	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL
rs4400148	ERAP1	cis	cerebellum	SCAN
rs4400148	CAST	cis	parietal	SCAN
rs4400148	LRAP	cis	multi-tissue	Pritchard

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95982800-95989600	Enhancers	Monocytes-CD14+_RO01746	blood
2	chr5:95983200-95994200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr5:95983800-95990800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:95984400-95989200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:95984800-95989400	Enhancers	Placenta Amnion	Placenta Amnion
6	chr5:95984800-95991000	Weak transcription	Psoas Muscle	Psoas
7	chr5:95984800-95991400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:95985400-95992000	Weak transcription	Pancreas	Pancrea
9	chr5:95985600-95990200	Weak transcription	A549	lung
10	chr5:95986000-95990800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:95986000-95990800	Weak transcription	Osteobl	bone
12	chr5:95986000-95991000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:95986000-95991000	Weak transcription	Liver	Liver
14	chr5:95986200-95990200	Weak transcription	HSMM	muscle
15	chr5:95986200-95990800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:95986200-95992000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:95986200-95992000	Weak transcription	Fetal Intestine Small	intestine
18	chr5:95986200-95992000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr5:95986400-95991000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr5:95986600-95991000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:95986600-95992000	Weak transcription	Fetal Intestine Large	intestine
22	chr5:95987400-95990800	Weak transcription	Brain Hippocampus Middle	brain
23	chr5:95987600-95989400	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr5:95987800-95989200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:95987800-95989400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr5:95988000-95988800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr5:95988000-95989000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr5:95988200-95988800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr5:95988200-95988800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr5:95988200-95988800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:95988200-95989000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr5:95988200-95989000	Enhancers	NHLF	lung
33	chr5:95988200-95989200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:95988200-95989200	Enhancers	Placenta	Placenta
35	chr5:95988200-95989400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:95988200-95989400	Enhancers	HMEC	breast
37	chr5:95988200-95989600	Enhancers	Hela-S3	cervix
38	chr5:95988400-95989000	Enhancers	Fetal Lung	lung
39	chr5:95988400-95989200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr5:95988400-95989200	Enhancers	Fetal Kidney	kidney
41	chr5:95988400-95989200	Enhancers	NHDF-Ad	bronchial
42	chr5:95988400-95989400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr5:95988400-95989400	Enhancers	NH-A	brain
44	chr5:95988400-95994600	Enhancers	NHEK	skin
45	chr5:95988600-95988800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
46	chr5:95988600-95988800	Flanking Active TSS	Esophagus	oesophagus
47	chr5:95988600-95989400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links