Variant report

Variant	rs3820097
Chromosome Location	chr1:161049358-161049359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161049267..161049804-chr1:161067227..161068374,4	MCF-7	breast:
2	chr1:161020801..161022470-chr1:161048503..161051319,2	K562	blood:
3	chr1:161043261..161046256-chr1:161047993..161050250,2	K562	blood:
4	chr1:161007186..161008951-chr1:161048410..161050017,2	MCF-7	breast:
5	chr1:161012288..161019472-chr1:161047717..161055328,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270149	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000143217	Chromatin interaction
ENSG00000215845	Chromatin interaction
ENSG00000158773	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10908822	0.95[ASN][1000 genomes]
rs11265547	0.95[ASN][1000 genomes]
rs11265549	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12142854	0.94[ASN][1000 genomes]
rs12401309	1.00[ASW][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1467742	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1556257	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3892376	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4233364	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4656285	1.00[CHB][hapmap];0.93[JPT][hapmap];0.98[ASN][1000 genomes]
rs4656287	0.92[GIH][hapmap];0.91[MEX][hapmap]
rs4656288	0.88[GIH][hapmap];0.82[MEX][hapmap]
rs4656978	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6671492	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv947135	chr1:161041002-161050287	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3820097	RXFP4	cis	parietal	SCAN
rs3820097	F11R	cis	cerebellum	SCAN
rs3820097	NIT1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161039600-161066800	Weak transcription	Right Atrium	heart
2	chr1:161039800-161052600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:161039800-161053000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:161040200-161052600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:161040200-161052800	Weak transcription	Colonic Mucosa	Colon
6	chr1:161042400-161049400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr1:161043600-161052800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:161043800-161050000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:161043800-161052200	Weak transcription	Spleen	Spleen
10	chr1:161045000-161050400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:161045000-161050800	Weak transcription	HSMM	muscle
12	chr1:161045000-161052400	Weak transcription	A549	lung
13	chr1:161045000-161053200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:161046400-161050000	Weak transcription	NHEK	skin
15	chr1:161046400-161050600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:161046600-161049400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:161046800-161049400	Weak transcription	HMEC	breast
18	chr1:161046800-161050200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:161047400-161053400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:161047600-161050200	Weak transcription	Stomach Mucosa	stomach
21	chr1:161047600-161052200	Weak transcription	Pancreas	Pancrea
22	chr1:161047600-161053000	Weak transcription	HepG2	liver
23	chr1:161048800-161049800	Genic enhancers	Placenta	Placenta
24	chr1:161048800-161050000	Genic enhancers	Esophagus	oesophagus
25	chr1:161049000-161049400	Genic enhancers	Placenta Amnion	Placenta Amnion
26	chr1:161049000-161049600	ZNF genes & repeats	Lung	lung
27	chr1:161049000-161055000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:161049200-161049400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:161049200-161049600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:161049200-161049600	Strong transcription	Gastric	stomach
31	chr1:161049200-161049800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:161049200-161050000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:161049200-161055600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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