Variant report

Variant	rs2022395
Chromosome Location	chr1:94607473-94607474
allele	A/C
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	POLR2A	chr1:94607452-94608213	HUVEC	blood vessel:	n/a	n/a
2	FOS	chr1:94607454-94608103	HUVEC	blood vessel:	n/a	chr1:94607791-94607799 chr1:94607792-94607799 chr1:94607790-94607800 chr1:94607790-94607800 chr1:94607791-94607799 chr1:94607790-94607800 chr1:94607789-94607800
3	FOSL2	chr1:94607469-94608174	SK-N-SH	brain:	n/a	chr1:94607791-94607799 chr1:94607792-94607799 chr1:94607790-94607800 chr1:94607790-94607800 chr1:94607791-94607799 chr1:94607790-94607800

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94596499..94598702-chr1:94606759..94609677,2	K562	blood:

Variant related genes	Relation type
ENSG00000233482	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1330861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1411704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2022396	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4847286	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4847287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs871662	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs871664	0.80[MEX][hapmap]
rs914063	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv871416	chr1:94566311-94635028	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv870932	chr1:94579053-94607607	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv871502	chr1:94579426-94607607	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv871306	chr1:94579426-94609478	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv871210	chr1:94579426-94629643	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2022395	IGF2BP3	trans	parietal	SCAN
rs2022395	HFM1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94600600-94612200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:94606400-94609200	Enhancers	HUVEC	blood vessel
3	chr1:94607000-94608600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:94607200-94607800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:94607200-94608000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:94607200-94608200	Enhancers	Muscle Satellite Cultured Cells	--
7	chr1:94607200-94608200	Enhancers	NHLF	lung
8	chr1:94607200-94608200	Enhancers	Osteobl	bone
9	chr1:94607200-94608400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:94607200-94608400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:94607200-94608400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:94607200-94608400	Enhancers	HSMM	muscle
13	chr1:94607200-94608400	Enhancers	NH-A	brain
14	chr1:94607200-94608600	Enhancers	HSMMtube	muscle
15	chr1:94607200-94608800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:94607200-94609200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:94607400-94607800	Enhancers	Brain Hippocampus Middle	brain
18	chr1:94607400-94607800	Enhancers	A549	lung
19	chr1:94607400-94607800	Flanking Active TSS	NHDF-Ad	bronchial
20	chr1:94607400-94607800	Enhancers	NHEK	skin
21	chr1:94607400-94608000	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr1:94607400-94608400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:94607400-94609200	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links