Variant report

Variant	rs868961
Chromosome Location	chr7:66437208-66437209
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10273658	0.91[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10807707	0.86[EUR][1000 genomes]
rs12534637	0.87[EUR][1000 genomes]
rs17680744	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1830070	0.86[EUR][1000 genomes]
rs4236209	0.83[EUR][1000 genomes]
rs4718421	0.86[EUR][1000 genomes]
rs4718428	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6460317	0.85[EUR][1000 genomes]
rs6961020	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6971897	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1032575	chr7:66432853-66576034	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs868961	RP4-756H11.3	cis	Thyroid	GTEx
rs868961	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs868961	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs868961	GUSB	cis	cerebellum	SCAN
rs868961	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs868961	GUSB	cis	parietal	SCAN
rs868961	RP4-756H11.3	cis	Artery Tibial	GTEx
rs868961	CRCP	cis	cerebellum	SCAN
rs868961	BBS4	trans	parietal	SCAN
rs868961	CRCP	cis	parietal	SCAN
rs868961	RP4-756H11.3	cis	lung	GTEx
rs868961	RP4-756H11.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66420600-66459200	Weak transcription	Psoas Muscle	Psoas
2	chr7:66424400-66439600	Weak transcription	K562	blood
3	chr7:66425800-66437800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr7:66426400-66453200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:66427000-66444800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:66427200-66438200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr7:66428200-66438000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:66433200-66458600	Weak transcription	Right Atrium	heart
9	chr7:66435200-66438200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr7:66435200-66438800	Enhancers	Fetal Intestine Small	intestine
11	chr7:66436000-66438000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr7:66436000-66440000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:66436000-66440200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr7:66437200-66437400	Enhancers	Gastric	stomach
15	chr7:66437200-66438200	Flanking Active TSS	HepG2	liver
16	chr7:66437200-66438600	Enhancers	Fetal Intestine Large	intestine
17	chr7:66437200-66439000	Enhancers	Stomach Mucosa	stomach

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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