Variant report

Variant	rs2843017
Chromosome Location	chr1:120318021-120318022
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:120307185..120310919-chr1:120314740..120318225,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134240	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1163542	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1163543	0.97[EUR][1000 genomes]
rs1163544	0.97[EUR][1000 genomes]
rs1163550	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1177389	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123085	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12132674	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1660607	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1814447	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582779	0.98[EUR][1000 genomes]
rs2582780	0.97[EUR][1000 genomes]
rs2582782	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2582784	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2582785	0.95[CEU][hapmap];0.99[EUR][1000 genomes]
rs2582786	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2582790	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2843014	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2843015	0.96[CEU][hapmap];0.98[EUR][1000 genomes]
rs2843016	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56239558	0.89[ASN][1000 genomes]
rs61789690	0.85[ASN][1000 genomes]
rs72695189	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs753425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935060	1.00[EUR][1000 genomes]
rs978730	0.98[EUR][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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer 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	11 gene(s)	inside rSNPs	diseases
4	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120311600-120318800	Enhancers	Fetal Intestine Large	intestine
2	chr1:120311800-120319600	Enhancers	Fetal Intestine Small	intestine
3	chr1:120311800-120324800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:120311800-120325400	Weak transcription	Lung	lung
5	chr1:120312000-120318600	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr1:120314400-120322600	Weak transcription	Right Atrium	heart
7	chr1:120314600-120321800	Weak transcription	Fetal Stomach	stomach
8	chr1:120314600-120324800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:120315200-120318400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:120315600-120318400	Enhancers	Stomach Mucosa	stomach
11	chr1:120315800-120318200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr1:120315800-120322000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:120316400-120318400	Enhancers	Liver	Liver
14	chr1:120316800-120319200	Weak transcription	Adipose Nuclei	Adipose
15	chr1:120316800-120322000	Weak transcription	Ovary	ovary
16	chr1:120316800-120322400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:120316800-120322600	Weak transcription	Left Ventricle	heart
18	chr1:120316800-120322600	Weak transcription	Psoas Muscle	Psoas
19	chr1:120316800-120322600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:120316800-120326000	Weak transcription	Esophagus	oesophagus
21	chr1:120317000-120321800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:120317000-120322000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr1:120317000-120322200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:120317000-120322400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:120317000-120322400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:120317000-120322600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:120317000-120322600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:120317000-120322600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:120317000-120322600	Weak transcription	NHEK	skin
30	chr1:120317000-120325400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:120317200-120318400	Enhancers	Placenta	Placenta
32	chr1:120317200-120322200	Weak transcription	Fetal Heart	heart
33	chr1:120317400-120321000	Weak transcription	Fetal Kidney	kidney
34	chr1:120317400-120321600	Weak transcription	Fetal Lung	lung
35	chr1:120317400-120322000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:120317400-120322000	Weak transcription	Fetal Muscle Leg	muscle
37	chr1:120317400-120322400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:120317600-120318200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:120317600-120318400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr1:120317600-120318400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:120317800-120318200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:120317800-120318200	Enhancers	Small Intestine	intestine
43	chr1:120317800-120318400	Enhancers	Pancreas	Pancrea
44	chr1:120317800-120318400	Flanking Active TSS	HepG2	liver
45	chr1:120318000-120318400	Enhancers	Duodenum Mucosa	Duodenum
46	chr1:120318000-120318400	Enhancers	Gastric	stomach
47	chr1:120318000-120318400	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr1:120318000-120318400	Genic enhancers	Hela-S3	cervix
49	chr1:120318000-120318600	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr1:120318000-120319000	Enhancers	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links