Variant report

Variant	rs11561916
Chromosome Location	chr7:147610923-147610924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11561915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761543	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11771110	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11980029	0.93[JPT][hapmap]
rs12533758	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13225365	1.00[YRI][hapmap]
rs13234998	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13235220	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13243566	0.82[YRI][hapmap]
rs17237331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1861009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2215798	0.93[JPT][hapmap]
rs2538964	0.89[CEU][hapmap]
rs2538973	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap]
rs2708244	0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2708259	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2710101	1.00[CEU][hapmap];0.93[JPT][hapmap]
rs2710103	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2710106	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2710109	0.94[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs34126004	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34902210	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57708946	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58175733	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6946545	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs7794222	0.85[GIH][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	nsv1023913	chr7:147521075-147806318	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1026058	chr7:147521109-147783042	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv539179	chr7:147521109-147783042	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv934002	chr7:147521110-147807705	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1017610	chr7:147523752-147806427	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11561916	C7orf29	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:147607000-147612400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:147607200-147612200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr7:147607200-147612600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:147608600-147612200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:147608600-147612400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr7:147609000-147611000	Enhancers	Fetal Muscle Leg	muscle
7	chr7:147609000-147612200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr7:147609200-147611000	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr7:147609400-147611000	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr7:147610200-147612000	Weak transcription	Adipose Nuclei	Adipose

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