Variant report

Variant	rs6946044
Chromosome Location	chr7:71362200-71362201
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10447536	0.89[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[ASN][1000 genomes]
rs10950286	0.95[CEU][hapmap];0.88[CHB][hapmap];0.88[GIH][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11763822	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11766067	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs11766746	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11769248	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11772460	0.91[ASN][1000 genomes]
rs11773010	0.80[ASN][1000 genomes]
rs12537432	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12537492	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs16869589	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs17144059	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs17340451	0.89[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs17340639	0.89[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.80[ASN][1000 genomes]
rs17424992	0.89[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs17425888	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2023987	0.82[JPT][hapmap]
rs2051883	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2051884	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2158656	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2867559	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35991621	0.80[ASN][1000 genomes]
rs56341267	0.80[ASN][1000 genomes]
rs59392444	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59411355	0.80[ASN][1000 genomes]
rs66494751	0.80[ASN][1000 genomes]
rs66607901	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67172404	0.93[ASN][1000 genomes]
rs67293403	0.80[ASN][1000 genomes]
rs6944606	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6956808	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6956922	0.95[ASN][1000 genomes]
rs6961118	0.80[ASN][1000 genomes]
rs6961327	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6965098	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6967264	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6968074	0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6969870	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs726469	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs73185015	0.80[ASN][1000 genomes]
rs733909	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7349979	0.89[CHB][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap]
rs769022	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.95[ASN][1000 genomes]
rs7776793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.95[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
rs6946044	CLIP2	cis	parietal	SCAN

Chromatin state (count:14 , 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	chr7:71360200-71363000	Enhancers	Primary hematopoietic stem cells	blood
4	chr7:71360200-71366200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr7:71360600-71362400	Enhancers	Brain Cingulate Gyrus	brain
6	chr7:71360600-71365800	Enhancers	Dnd41	blood
7	chr7:71360800-71362200	Enhancers	Brain Hippocampus Middle	brain
8	chr7:71360800-71362600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:71361000-71362400	Enhancers	Brain Substantia Nigra	brain
10	chr7:71361000-71362800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr7:71361600-71362200	Enhancers	Adipose Nuclei	Adipose
12	chr7:71361800-71362200	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr7:71362000-71362200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr7:71362200-71366800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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