Variant report

Variant	rs7580900
Chromosome Location	chr2:231081384-231081385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL11A	chr2:231081280-231081473	GM12878	blood:	n/a	n/a
2	RUNX3	chr2:231081231-231081647	GM12878	blood:	n/a	chr2:231081420-231081429 chr2:231081420-231081429 chr2:231081414-231081429
3	EBF1	chr2:231081302-231081558	GM12878	blood:	n/a	n/a
4	FOXM1	chr2:231081167-231081583	GM12878	blood:	n/a	n/a
5	BATF	chr2:231081292-231081652	GM12878	blood:	n/a	n/a
6	RUNX3	chr2:231081129-231081640	GM12878	blood:	n/a	chr2:231081420-231081429 chr2:231081420-231081429 chr2:231081414-231081429
7	IKZF1	chr2:231081223-231081555	GM12878	blood:	n/a	n/a
8	NFIC	chr2:231081072-231081688	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:231072082..231074333-chr2:231080031..231082815,2	MCF-7	breast:
2	chr2:231080762..231082857-chr2:231083207..231085642,2	K562	blood:

Variant related genes	Relation type
SP110	TF binding region
ENSG00000135899	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1465530	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1863675	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1966555	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114589	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2278197	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs28399164	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3813466	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4143559	0.86[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4384773	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4973303	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs56936337	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6708519	0.98[ASN][1000 genomes]
rs7581442	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9288660	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap]
rs9288661	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001562	chr2:230862717-231187043	Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv536156	chr2:230862717-231187043	Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv498047	chr2:230951712-231250489	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv869834	chr2:231045013-231139827	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv998291	chr2:231045388-231136278	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584666	chr2:231050715-231106621	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7580900	NGEF	cis	parietal	SCAN
rs7580900	SP140	cis	lymphoblastoid	seeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231059000-231082800	Weak transcription	Stomach Mucosa	stomach
2	chr2:231062200-231081600	Strong transcription	Liver	Liver
3	chr2:231062400-231081600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:231062600-231081400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:231062600-231081400	Strong transcription	Adipose Nuclei	Adipose
6	chr2:231062600-231081400	Strong transcription	Duodenum Smooth Muscle	Duodenum
7	chr2:231062600-231081400	Strong transcription	Fetal Thymus	thymus
8	chr2:231062600-231081600	Strong transcription	Fetal Lung	lung
9	chr2:231062600-231081600	Strong transcription	Placenta	Placenta
10	chr2:231062600-231081600	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr2:231062600-231081600	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:231062600-231081800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr2:231062600-231082200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:231062600-231082400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:231062600-231084200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:231063000-231084000	Weak transcription	Hela-S3	cervix
17	chr2:231063200-231084000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:231063400-231082200	Strong transcription	Fetal Muscle Leg	muscle
19	chr2:231064800-231084000	Weak transcription	Fetal Heart	heart
20	chr2:231065000-231081400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:231066200-231083200	Weak transcription	HUVEC	blood vessel
22	chr2:231066200-231084400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:231066400-231081600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:231067000-231081400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr2:231067200-231081600	Strong transcription	Left Ventricle	heart
26	chr2:231067600-231084200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:231068200-231082200	Strong transcription	Ovary	ovary
28	chr2:231068200-231084400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:231068400-231081800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:231068400-231084000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:231069400-231081600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:231070200-231081600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:231070800-231081600	Strong transcription	Lung	lung
34	chr2:231071800-231084200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:231072400-231081600	Strong transcription	Fetal Stomach	stomach
36	chr2:231073200-231081600	Strong transcription	Right Ventricle	heart
37	chr2:231073600-231084000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:231074200-231084000	Weak transcription	Fetal Kidney	kidney
39	chr2:231074800-231081800	Strong transcription	Spleen	Spleen
40	chr2:231075200-231081800	Strong transcription	Thymus	Thymus
41	chr2:231075400-231081400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:231075400-231082000	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr2:231076000-231081800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr2:231076000-231084200	Weak transcription	Brain Angular Gyrus	brain
45	chr2:231076800-231081600	Strong transcription	Colon Smooth Muscle	Colon
46	chr2:231076800-231084000	Weak transcription	NHDF-Ad	bronchial
47	chr2:231077400-231084000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr2:231077400-231084000	Weak transcription	NH-A	brain
49	chr2:231077400-231084000	Weak transcription	Osteobl	bone
50	chr2:231077400-231084200	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links