Variant report

Variant	rs4953447
Chromosome Location	chr2:47263232-47263233
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47243930..47246637-chr2:47261701..47264377,2	MCF-7	breast:
2	chr2:47261315..47264096-chr2:47264626..47268326,4	K562	blood:
3	chr2:47262955..47263771-chr2:47304202..47304764,2	MCF-7	breast:
4	chr2:47260087..47265958-chr2:47400378..47404964,8	K562	blood:
5	chr2:47262016..47264669-chr2:47272967..47274595,2	MCF-7	breast:
6	chr2:47252232..47263251-chr2:47397787..47406051,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068724	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000233845	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11125113	0.81[EUR][1000 genomes]
rs12617529	0.82[JPT][hapmap]
rs1865257	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2304289	0.83[GIH][hapmap];0.91[JPT][hapmap]
rs2304290	0.80[GIH][hapmap];0.81[JPT][hapmap]
rs3739100	0.81[CHB][hapmap]
rs4952862	0.83[GIH][hapmap];0.86[JPT][hapmap]
rs4952863	0.82[JPT][hapmap]
rs4953445	0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4953446	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4953448	0.87[ASW][hapmap];0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs6717063	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7575628	1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs892377	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs892378	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs892379	0.87[JPT][hapmap];0.82[ASN][1000 genomes]

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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv984532	chr2:47237908-47270533	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv457363	chr2:47249239-47263232	Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv581753	chr2:47249239-47263232	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv528091	chr2:47249239-47273732	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4953447	SOCS5	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47230200-47302800	Strong transcription	Dnd41	blood
2	chr2:47232000-47265000	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr2:47234400-47283600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:47236000-47278600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:47245800-47268600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:47246000-47283800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:47246800-47281600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:47251600-47265000	Strong transcription	Primary T cells from cord blood	blood
9	chr2:47251600-47266000	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr2:47252000-47283400	Strong transcription	Thymus	Thymus
11	chr2:47255600-47273400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:47256800-47264000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:47257000-47277000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:47257600-47265200	Genic enhancers	Spleen	Spleen
15	chr2:47257600-47267800	Genic enhancers	Fetal Muscle Leg	muscle
16	chr2:47258400-47268400	Genic enhancers	Fetal Thymus	thymus
17	chr2:47258400-47282600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:47258600-47263400	Enhancers	Liver	Liver
19	chr2:47258600-47263400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr2:47258600-47265200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:47258800-47263400	Enhancers	Left Ventricle	heart
22	chr2:47259000-47263800	Enhancers	Fetal Heart	heart
23	chr2:47259200-47263400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr2:47259200-47263400	Genic enhancers	Fetal Intestine Small	intestine
25	chr2:47259200-47263400	Enhancers	Fetal Kidney	kidney
26	chr2:47259200-47263600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:47259200-47265000	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr2:47259400-47263400	Enhancers	Right Ventricle	heart
29	chr2:47259400-47265000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:47259400-47266800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr2:47259600-47263400	Enhancers	Colon Smooth Muscle	Colon
32	chr2:47259600-47263400	Enhancers	Pancreas	Pancrea
33	chr2:47259600-47295000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:47259800-47263600	Enhancers	Fetal Intestine Large	intestine
35	chr2:47260000-47266000	Enhancers	Placenta	Placenta
36	chr2:47260200-47264600	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr2:47260400-47263400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr2:47260400-47263400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr2:47260800-47263800	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr2:47260800-47264000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:47261000-47263400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:47261000-47263400	Enhancers	Colonic Mucosa	Colon
43	chr2:47261000-47264000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:47261000-47264000	Enhancers	Adipose Nuclei	Adipose
45	chr2:47261000-47264200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:47261000-47266000	Weak transcription	Aorta	Aorta
47	chr2:47261200-47263600	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr2:47261400-47263400	Genic enhancers	GM12878-XiMat	blood
49	chr2:47261600-47263800	Enhancers	Primary B cells from cord blood	blood
50	chr2:47261600-47263800	Enhancers	Brain Hippocampus Middle	brain

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