Variant report

Variant	rs17238968
Chromosome Location	chr4:62256068-62256069
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10032294	0.86[YRI][hapmap]
rs1032896	0.93[YRI][hapmap]
rs1456862	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs28415588	0.93[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs28491363	0.91[ASN][1000 genomes]
rs28628386	0.90[ASN][1000 genomes]
rs28705222	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2880363	0.93[YRI][hapmap]
rs4860091	0.93[YRI][hapmap]
rs9312076	0.93[ASW][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.83[LWK][hapmap];0.94[MKK][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9992321	0.95[AFR][1000 genomes];0.90[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	nsv879075	chr4:62124531-62354791	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv461376	chr4:62187646-62274626	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv594327	chr4:62187646-62274626	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv868844	chr4:62241702-62497248	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv879076	chr4:62251077-62354791	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17238968	IGFBP7	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:62247600-62262200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:62251200-62263000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:62251200-62266200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr4:62254600-62256400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr4:62254600-62273400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr4:62255200-62256200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr4:62255200-62260000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:62255200-62263000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr4:62255400-62256200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:62255600-62256200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr4:62255600-62257000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:62255600-62258600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:62255600-62260800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:62255600-62261400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:62255600-62261600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:62255600-62266200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:62255800-62260400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr4:62255800-62260800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:62256000-62256200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:62256000-62256400	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links