Variant report

Variant	rs6126982
Chromosome Location	chr20:52456445-52456446
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:70148331..70150466-chr20:52456396..52458617,2	MCF-7	breast:
2	chr20:52455663..52458624-chr20:52464778..52466415,2	K562	blood:
3	chr17:57920608..57923011-chr20:52454169..52456607,2	MCF-7	breast:
4	chr20:52455023..52457769-chr20:52462367..52464597,2	K562	blood:

Variant related genes	Relation type
ENSG00000127328	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10432728	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4809941	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4809942	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4811475	0.80[ASN][1000 genomes]
rs4811476	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6013809	0.85[JPT][hapmap]
rs6022786	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs6022793	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6064010	0.88[ASN][1000 genomes]
rs6064011	0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs6068684	0.84[JPT][hapmap]
rs6068688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6068690	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6068691	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs6091756	0.83[ASN][1000 genomes]
rs6097618	0.89[CEU][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs6097632	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6123320	0.85[ASN][1000 genomes]
rs6126985	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6126986	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs720387	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases
5	esv1831516	chr20:52437245-52514913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6126982	NFATC2	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52447400-52459400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr20:52449600-52457800	Enhancers	Primary B cells from cord blood	blood
3	chr20:52449800-52461000	Enhancers	Primary B cells from peripheral blood	blood
4	chr20:52450000-52462000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr20:52450400-52457800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr20:52450400-52465200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr20:52450600-52465200	Enhancers	Primary T cells fromperipheralblood	blood
8	chr20:52451000-52457000	Weak transcription	NHDF-Ad	bronchial
9	chr20:52451000-52462600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr20:52451200-52457000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr20:52451200-52457200	Weak transcription	NHEK	skin
12	chr20:52451200-52464000	Weak transcription	HSMM	muscle
13	chr20:52452200-52456800	Enhancers	Fetal Intestine Large	intestine
14	chr20:52452400-52463800	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr20:52452400-52465200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr20:52452600-52461400	Weak transcription	Osteobl	bone
17	chr20:52453400-52456800	Enhancers	Fetal Intestine Small	intestine
18	chr20:52453600-52457200	Enhancers	Stomach Mucosa	stomach
19	chr20:52453600-52458000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr20:52453600-52480200	Weak transcription	Small Intestine	intestine
21	chr20:52454400-52457000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr20:52454400-52464200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr20:52454800-52457400	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr20:52454800-52457400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr20:52454800-52457800	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr20:52455000-52457000	Enhancers	Fetal Thymus	thymus
27	chr20:52455000-52457200	Enhancers	Dnd41	blood
28	chr20:52455000-52457400	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr20:52455000-52459000	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr20:52455000-52464800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr20:52455200-52456600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr20:52455200-52456600	Enhancers	Thymus	Thymus
33	chr20:52455400-52457000	Enhancers	Colonic Mucosa	Colon
34	chr20:52455600-52457400	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr20:52455800-52456600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr20:52455800-52456800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr20:52455800-52457000	Enhancers	Primary hematopoietic stem cells	blood
38	chr20:52455800-52457000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr20:52456000-52456600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr20:52456000-52456600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr20:52456000-52456600	Enhancers	Liver	Liver
42	chr20:52456000-52456600	Enhancers	Fetal Lung	lung
43	chr20:52456000-52456600	Enhancers	Fetal Muscle Trunk	muscle
44	chr20:52456000-52456600	Enhancers	Placenta	Placenta
45	chr20:52456000-52456600	Enhancers	Gastric	stomach
46	chr20:52456000-52456600	Enhancers	Pancreas	Pancrea
47	chr20:52456000-52456600	Flanking Active TSS	HepG2	liver
48	chr20:52456000-52457200	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr20:52456000-52457400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr20:52456200-52456600	Enhancers	H1 Cell Line	embryonic stem cell

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