Variant report

Variant	rs2764908
Chromosome Location	chr1:59348528-59348529
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:59346337..59348680-chr1:59454325..59456505,2	K562	blood:
2	chr1:59244354..59252225-chr1:59338738..59357283,49	K562	blood:
3	chr1:59242511..59252251-chr1:59329388..59355607,72	K562	blood:
4	chr1:59348233..59353011-chr1:59368695..59371190,6	K562	blood:
5	chr1:59334588..59339856-chr1:59347478..59351607,5	K562	blood:
6	chr1:59348022..59349569-chr1:59688240..59689878,2	K562	blood:
7	chr1:59271009..59273786-chr1:59347629..59349525,2	K562	blood:
8	chr1:59279129..59280859-chr1:59347455..59349368,2	K562	blood:
9	chr1:59271030..59273064-chr1:59348436..59350050,2	MCF-7	breast:
10	chr1:59280214..59283774-chr1:59346159..59349299,3	MCF-7	breast:
11	chr1:59347579..59349561-chr1:76189900..76191497,2	K562	blood:
12	chr1:59347205..59349550-chr1:59349872..59353035,4	K562	blood:
13	chr1:59348284..59350595-chr1:59436968..59439590,2	K562	blood:
14	chr1:59345982..59347514-chr1:59347634..59350108,2	MCF-7	breast:
15	chr1:59336458..59340838-chr1:59348278..59351607,4	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JUN-2	chr1:59348476-59349406	NONHSAT003536

No data

Variant related genes	Relation type
ENSG00000117054	Chromatin interaction
ENSG00000177606	Chromatin interaction
ENSG00000234807	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs17096897	0.89[MEX][hapmap]
rs1998761	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1998762	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2011623	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2492321	0.82[ASW][hapmap];0.86[CHB][hapmap];0.81[MKK][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2492323	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2716117	0.80[ASW][hapmap];0.82[AFR][1000 genomes]
rs2764909	0.82[ASW][hapmap];0.89[MEX][hapmap]
rs2999129	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2764908	NFIA	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59319800-59361400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:59340800-59348600	Weak transcription	Placenta	Placenta
3	chr1:59341000-59348600	Weak transcription	Fetal Brain Male	brain
4	chr1:59341200-59348600	Weak transcription	HSMMtube	muscle
5	chr1:59341200-59350200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:59341400-59348600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:59341600-59348800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:59344800-59356000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:59345000-59348600	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr1:59346200-59348800	Enhancers	Hela-S3	cervix
11	chr1:59346200-59348800	Enhancers	K562	blood
12	chr1:59346200-59350600	Enhancers	HepG2	liver
13	chr1:59346200-59353600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:59346200-59353800	Enhancers	Psoas Muscle	Psoas
15	chr1:59346400-59349800	Enhancers	HMEC	breast
16	chr1:59346400-59353400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:59346400-59354000	Enhancers	Fetal Intestine Small	intestine
18	chr1:59346600-59352000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:59346600-59352000	Enhancers	HUVEC	blood vessel
20	chr1:59346600-59354000	Enhancers	Fetal Intestine Large	intestine
21	chr1:59346800-59349000	Enhancers	NHLF	lung
22	chr1:59346800-59349800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:59346800-59351200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:59346800-59352000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr1:59346800-59353400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr1:59347000-59348800	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr1:59347000-59349000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:59347000-59349000	Enhancers	Duodenum Mucosa	Duodenum
29	chr1:59347000-59349000	Enhancers	Esophagus	oesophagus
30	chr1:59347000-59349600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:59347000-59349800	Enhancers	Osteobl	bone
32	chr1:59347000-59350000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:59347000-59350000	Enhancers	NHEK	skin
34	chr1:59347000-59350400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:59347000-59351200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr1:59347000-59352000	Enhancers	Liver	Liver
37	chr1:59347000-59352000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr1:59347000-59352600	Enhancers	NH-A	brain
39	chr1:59347000-59352800	Enhancers	Left Ventricle	heart
40	chr1:59347000-59353200	Enhancers	Stomach Mucosa	stomach
41	chr1:59347000-59353400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr1:59347000-59353800	Enhancers	Lung	lung
43	chr1:59347000-59353800	Enhancers	Right Atrium	heart
44	chr1:59347000-59354800	Enhancers	NHDF-Ad	bronchial
45	chr1:59347200-59349400	Enhancers	Adipose Nuclei	Adipose
46	chr1:59347200-59349600	Enhancers	HSMM	muscle
47	chr1:59347200-59349800	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr1:59347200-59351400	Enhancers	Brain Cingulate Gyrus	brain
49	chr1:59347200-59353800	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr1:59347200-59354000	Enhancers	Pancreas	Pancrea

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