Variant report

Variant	rs947273
Chromosome Location	chr1:120451352-120451353
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120449760..120452245-chrX:18130620..18132924,2	MCF-7	breast:
2	chr1:120450368..120452473-chr1:120481049..120483944,2	K562	blood:
3	chr1:120449201..120451980-chr1:120452971..120455460,2	MCF-7	breast:
4	chr1:120445705..120448547-chr1:120448757..120452152,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261662	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10494235	0.92[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923926	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923929	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493695	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493696	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1493698	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2027447	0.84[CEU][hapmap]
rs2453042	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453044	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453055	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2453056	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2487568	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493398	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493410	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493411	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493416	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2493419	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493420	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641316	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641338	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641346	0.84[CEU][hapmap]
rs2793823	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2793827	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793830	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs327196	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3897478	0.84[CEU][hapmap]
rs4659250	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5025718	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688004	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs699779	0.84[CEU][hapmap]
rs699780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835573	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835574	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835575	0.84[CEU][hapmap]
rs835576	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
4	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
5	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
6	nsv915933	chr1:120323527-120471049	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv831226	chr1:120331599-120471049	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv533996	chr1:120359524-120471049	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv436325	chr1:120390914-120471049	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv547625	chr1:120422705-120466108	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv2610	chr1:120451060-120471049	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120444600-120453000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:120446400-120452000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:120446400-120454400	Weak transcription	NH-A	brain
4	chr1:120446600-120453400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:120448200-120452600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:120448200-120471000	Weak transcription	Right Atrium	heart
7	chr1:120448400-120453200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:120448400-120457400	Weak transcription	Fetal Brain Female	brain
9	chr1:120448800-120454800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:120448800-120455800	Weak transcription	NHLF	lung
11	chr1:120448800-120456000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:120449000-120456600	Weak transcription	Aorta	Aorta
13	chr1:120449200-120452800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:120449200-120457200	Weak transcription	Gastric	stomach
15	chr1:120449400-120453000	Weak transcription	Esophagus	oesophagus
16	chr1:120449400-120453400	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:120449600-120456200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:120449600-120457800	Weak transcription	Fetal Intestine Small	intestine
19	chr1:120449800-120453400	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr1:120450000-120453400	Weak transcription	Osteobl	bone
21	chr1:120450000-120473000	Strong transcription	HSMM	muscle
22	chr1:120450200-120452600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:120450200-120453000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:120450200-120456200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:120450200-120457800	Weak transcription	Colonic Mucosa	Colon
26	chr1:120450200-120458600	Weak transcription	HepG2	liver
27	chr1:120450400-120453000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:120450400-120455200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:120450400-120455600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:120450400-120456800	Weak transcription	Fetal Intestine Large	intestine
31	chr1:120450400-120456800	Weak transcription	Pancreas	Pancrea
32	chr1:120450600-120453000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:120450600-120453000	Weak transcription	Fetal Stomach	stomach
34	chr1:120450600-120454400	Weak transcription	NHDF-Ad	bronchial
35	chr1:120450600-120455800	Weak transcription	Liver	Liver
36	chr1:120450800-120453400	Weak transcription	HSMMtube	muscle
37	chr1:120450800-120454400	Weak transcription	Primary B cells from cord blood	blood
38	chr1:120450800-120456600	Weak transcription	Thymus	Thymus
39	chr1:120451000-120452600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:120451000-120454800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:120451000-120455200	Weak transcription	Placenta	Placenta
42	chr1:120451000-120456600	Weak transcription	Spleen	Spleen
43	chr1:120451000-120458400	Weak transcription	Small Intestine	intestine
44	chr1:120451000-120466800	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links