Variant report

Variant	rs2522822
Chromosome Location	chr7:27068491-27068492
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:27061277-27071265..7:27203007-27207968	H1-hESC	embryonic stem cell:	embryo
2	7:27061277-27071265..7:27238414-27242313	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000078399	Chromatin interaction
ENSG00000106031	Chromatin interaction
ENSG00000243766	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1005977	0.91[EUR][1000 genomes]
rs10231265	0.93[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10267442	0.92[EUR][1000 genomes]
rs1082313	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11975480	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11977871	0.91[AFR][1000 genomes]
rs12700771	0.82[AFR][1000 genomes]
rs13311400	0.87[EUR][1000 genomes]
rs2015424	0.93[EUR][1000 genomes]
rs213520	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs213532	0.80[EUR][1000 genomes]
rs2252947	0.96[CEU][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes]
rs2264680	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2428420	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2428424	0.92[EUR][1000 genomes]
rs2428426	0.90[EUR][1000 genomes]
rs2428427	0.88[EUR][1000 genomes]
rs2428428	0.91[EUR][1000 genomes]
rs2428430	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2462901	0.92[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2462903	0.97[EUR][1000 genomes]
rs2462905	0.90[EUR][1000 genomes]
rs2462907	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs2465263	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs2465265	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2465267	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2522823	1.00[CEU][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2522829	0.96[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2693658	0.93[EUR][1000 genomes]
rs2693661	0.82[YRI][hapmap]
rs2693666	1.00[CEU][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2712231	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2712232	0.94[EUR][1000 genomes]
rs2712235	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2712240	0.92[EUR][1000 genomes]
rs2712241	1.00[CEU][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes]
rs2712243	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2712249	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2936426	0.87[EUR][1000 genomes]
rs2960784	0.87[EUR][1000 genomes]
rs2960786	0.87[EUR][1000 genomes]
rs774248	0.89[EUR][1000 genomes]
rs774254	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs774255	0.96[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs774264	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs774269	0.85[EUR][1000 genomes]
rs799237	0.96[CEU][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs954051	0.88[YRI][hapmap]

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	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv1018709	chr7:26990384-27216552	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
4	nsv538806	chr7:26990384-27216552	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	nsv967485	chr7:27066773-27082518	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2522822	SKAP2	cis	Whole Blood	GTEx
rs2522822	HOXA2	cis	Whole Blood	GTEx
rs2522822	HOTAIRM1	cis	Whole Blood	GTEx
rs2522822	HOXA-AS2	cis	Whole Blood	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27065200-27070200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr7:27068000-27068800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr7:27068200-27068600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr7:27068200-27068600	Enhancers	Fetal Kidney	kidney
5	chr7:27068200-27068800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr7:27068200-27068800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
7	chr7:27068200-27069200	Enhancers	Stomach Mucosa	stomach
8	chr7:27068200-27069400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
9	chr7:27068200-27071600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:27068400-27068600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:27068400-27068600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr7:27068400-27068600	Enhancers	Thymus	Thymus
13	chr7:27068400-27068600	Enhancers	HSMMtube	muscle
14	chr7:27068400-27068800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr7:27068400-27068800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
16	chr7:27068400-27068800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
17	chr7:27068400-27068800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
18	chr7:27068400-27071800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell

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