Variant report

Variant	rs2011623
Chromosome Location	chr1:59360403-59360404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:59242448..59252747-chr1:59356992..59375072,48	K562	blood:
2	chr1:59242448..59251438-chr1:59358057..59375559,39	K562	blood:

Variant related genes	Relation type
ENSG00000234807	Chromatin interaction
ENSG00000177606	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]
rs1886745	0.93[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs1998761	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1998762	0.82[EUR][1000 genomes]
rs2492321	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[ASN][1000 genomes]
rs2492323	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2764908	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]
rs2764909	0.89[MEX][hapmap]
rs2999129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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
rs2011623	NFIA	cis	parietal	SCAN

Chromatin state (count:68 , 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	chr1:59348000-59360800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:59351000-59360800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:59351800-59360800	Weak transcription	Fetal Heart	heart
5	chr1:59352400-59360800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:59352800-59360600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:59353400-59360800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:59353600-59361200	Weak transcription	Ovary	ovary
9	chr1:59354800-59360800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:59355000-59360800	Weak transcription	HSMMtube	muscle
11	chr1:59355200-59360800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:59355800-59360800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:59355800-59361000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:59355800-59361400	Weak transcription	NH-A	brain
15	chr1:59356000-59360800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:59356000-59361200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:59356200-59360800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:59356200-59368600	Weak transcription	Esophagus	oesophagus
19	chr1:59357800-59364200	Enhancers	K562	blood
20	chr1:59358200-59367200	Enhancers	HUVEC	blood vessel
21	chr1:59358400-59368600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:59358600-59361400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr1:59358600-59361400	Enhancers	Stomach Mucosa	stomach
24	chr1:59358600-59361800	Enhancers	Gastric	stomach
25	chr1:59358600-59367000	Enhancers	Adipose Nuclei	Adipose
26	chr1:59358800-59360800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:59358800-59361400	Enhancers	Duodenum Mucosa	Duodenum
28	chr1:59358800-59365800	Enhancers	Lung	lung
29	chr1:59358800-59367000	Enhancers	Fetal Muscle Leg	muscle
30	chr1:59359000-59360800	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr1:59359000-59361600	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr1:59359000-59363000	Enhancers	Fetal Muscle Trunk	muscle
33	chr1:59359000-59363600	Enhancers	Pancreas	Pancrea
34	chr1:59359000-59363800	Enhancers	Right Ventricle	heart
35	chr1:59359000-59365800	Enhancers	Left Ventricle	heart
36	chr1:59359000-59366400	Enhancers	Primary hematopoietic stem cells	blood
37	chr1:59359000-59367000	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr1:59359000-59367200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr1:59359000-59368600	Enhancers	Fetal Intestine Small	intestine
40	chr1:59359000-59368800	Enhancers	Fetal Intestine Large	intestine
41	chr1:59359200-59366400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:59359400-59361800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:59359400-59361800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr1:59359600-59360600	Weak transcription	HepG2	liver
45	chr1:59359600-59360600	Weak transcription	HSMM	muscle
46	chr1:59359600-59360800	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:59359600-59360800	Weak transcription	Brain Substantia Nigra	brain
48	chr1:59359600-59361000	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr1:59359600-59361200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:59359600-59365600	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links