Variant report

Variant	rs10950294
Chromosome Location	chr7:71555904-71555905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10215588	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10231333	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs10251441	0.83[JPT][hapmap]
rs10252717	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10254309	0.90[CHD][hapmap];0.91[JPT][hapmap]
rs10255136	0.87[CHD][hapmap];0.91[JPT][hapmap]
rs10260183	0.91[JPT][hapmap]
rs10260420	0.91[JPT][hapmap]
rs10260767	0.91[JPT][hapmap]
rs10281262	0.91[JPT][hapmap]
rs10807741	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10807742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10807744	1.00[JPT][hapmap]
rs10950291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10950292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10950293	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10950295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10950297	0.83[CHD][hapmap];0.91[JPT][hapmap]
rs10950298	0.91[JPT][hapmap]
rs11760663	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs11765179	0.83[JPT][hapmap]
rs11767138	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11772246	1.00[JPT][hapmap]
rs11772542	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972568	0.91[JPT][hapmap]
rs11975544	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs11982267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11983124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12531663	0.88[JPT][hapmap]
rs12538529	0.91[JPT][hapmap]
rs12666578	0.91[JPT][hapmap]
rs12673109	0.83[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs13224539	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs13227792	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13231944	0.81[ASN][1000 genomes]
rs13239589	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs17144357	0.90[JPT][hapmap]
rs1852088	0.86[ASN][1000 genomes]
rs1852089	0.86[ASN][1000 genomes]
rs2016778	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2040869	0.91[JPT][hapmap]
rs2867567	0.90[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2867569	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33986788	0.81[ASN][1000 genomes]
rs34655504	0.83[JPT][hapmap]
rs34801868	0.83[JPT][hapmap]
rs34862805	0.87[ASN][1000 genomes]
rs34913023	0.84[ASN][1000 genomes]
rs35830920	0.85[ASN][1000 genomes]
rs35897134	0.81[ASN][1000 genomes]
rs4457209	0.91[JPT][hapmap]
rs4717628	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs4719207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4719209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4719216	1.00[JPT][hapmap]
rs55895910	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56410383	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58547626	0.84[ASN][1000 genomes]
rs59086558	0.81[ASN][1000 genomes]
rs59738349	0.81[ASN][1000 genomes]
rs60902167	0.81[ASN][1000 genomes]
rs61193914	0.81[ASN][1000 genomes]
rs6952558	1.00[JPT][hapmap]
rs6959686	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs6963114	0.90[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs71551247	0.87[ASN][1000 genomes]
rs73124358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73124360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73124365	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73124374	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73124389	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7796985	0.87[ASN][1000 genomes]
rs7797796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799436	0.83[JPT][hapmap]
rs844749	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv491610	chr7:71422560-71803630	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv831023	chr7:71443549-71588033	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv531373	chr7:71487076-71765613	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv817506	chr7:71488542-71935721	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1034282	chr7:71531113-71876617	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1015848	chr7:71552185-71736068	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv538942	chr7:71552185-71736068	ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10950294	CLDN3	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:71553000-71563000	Weak transcription	Thymus	Thymus
2	chr7:71553200-71559000	Weak transcription	Fetal Thymus	thymus
3	chr7:71555600-71558600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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