Variant report

Variant	rs6460694
Chromosome Location	chr7:71361036-71361037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10242189	0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10950284	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10950285	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11763757	0.81[TSI][hapmap]
rs11767496	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11770636	0.80[ASN][1000 genomes]
rs12154985	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12164040	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13229300	0.84[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs17144084	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17144086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1986017	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2051885	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2107880	0.89[ASN][1000 genomes]
rs2214747	0.87[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2867522	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867560	0.80[ASN][1000 genomes]
rs33946733	0.81[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs4717619	0.86[ASN][1000 genomes]
rs60530198	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6460693	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6460695	0.90[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs6958157	0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6959613	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6964517	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6966229	0.88[ASN][1000 genomes]
rs6976024	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7785844	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs7795294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7795444	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7811694	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7812085	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9638637	1.00[JPT][hapmap];0.85[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	nsv1026896	chr7:71003462-71721516	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1027496	chr7:71162362-71575116	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916220	chr7:71200006-71708048	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv531372	chr7:71300090-71909517	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv1017367	chr7:71339782-71476575	ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6460694	CLIP2	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:71352000-71365400	Weak transcription	Fetal Thymus	thymus
2	chr7:71354000-71365400	Weak transcription	Thymus	Thymus
3	chr7:71358400-71361600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:71360000-71361600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr7:71360200-71363000	Enhancers	Primary hematopoietic stem cells	blood
6	chr7:71360200-71366200	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr7:71360600-71362400	Enhancers	Brain Cingulate Gyrus	brain
8	chr7:71360600-71365800	Enhancers	Dnd41	blood
9	chr7:71360800-71362200	Enhancers	Brain Hippocampus Middle	brain
10	chr7:71360800-71362600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:71361000-71361800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:71361000-71361800	Enhancers	Brain Angular Gyrus	brain
13	chr7:71361000-71362000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr7:71361000-71362400	Enhancers	Brain Substantia Nigra	brain
15	chr7:71361000-71362800	Enhancers	Primary neutrophils fromperipheralblood	blood

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