Variant report

Variant	rs4717628
Chromosome Location	chr7:71615845-71615846
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10215588	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs10231333	0.82[JPT][hapmap]
rs10251441	0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs10254309	0.82[JPT][hapmap]
rs10255136	0.82[JPT][hapmap]
rs10260183	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs10260420	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs10260767	0.85[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs10274714	0.83[ASN][1000 genomes]
rs10280044	0.83[ASN][1000 genomes]
rs10281262	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs10807742	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs10807743	0.83[ASN][1000 genomes]
rs10807744	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10950291	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs10950294	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs10950295	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs10950297	0.82[JPT][hapmap]
rs10950298	0.85[CHD][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs10950301	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11760663	0.87[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11765179	1.00[ASW][hapmap];0.83[CEU][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs11767811	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772246	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11773728	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11972568	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs11982267	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11983124	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs12531663	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12538529	0.88[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12666578	0.82[JPT][hapmap]
rs13224539	0.82[JPT][hapmap]
rs13235059	0.81[ASN][1000 genomes]
rs13239589	0.82[JPT][hapmap]
rs17144357	1.00[CEU][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17144373	0.84[JPT][hapmap]
rs2040869	0.82[JPT][hapmap]
rs2079318	0.84[ASN][1000 genomes]
rs2867567	0.82[JPT][hapmap]
rs34310597	0.82[ASN][1000 genomes]
rs34655504	0.85[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs34853510	0.87[AFR][1000 genomes]
rs4457209	0.85[CHD][hapmap];0.82[JPT][hapmap]
rs4719207	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs4719209	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs4719215	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4719216	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4719219	0.83[EUR][1000 genomes]
rs4719220	0.86[TSI][hapmap];0.88[YRI][hapmap]
rs6952558	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6959686	0.82[JPT][hapmap]
rs6963114	0.82[JPT][hapmap]
rs6978130	0.82[EUR][1000 genomes]
rs73127982	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73130009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73141552	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73141560	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73141567	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7788950	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7797796	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs7799436	0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs959405	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv831024	chr7:71569349-71735250	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1023496	chr7:71593461-71633053	Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv529620	chr7:71604785-71935721	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4717628	CALN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:71607600-71617600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr7:71607800-71616600	Weak transcription	Thymus	Thymus
3	chr7:71612000-71616600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:71614200-71616000	Weak transcription	Fetal Thymus	thymus
5	chr7:71614600-71619600	Enhancers	Brain Anterior Caudate	brain
6	chr7:71614600-71619800	Enhancers	Brain Substantia Nigra	brain
7	chr7:71614800-71617200	Enhancers	Brain Cingulate Gyrus	brain
8	chr7:71614800-71617400	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr7:71615000-71616600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:71615000-71617400	Enhancers	Brain Hippocampus Middle	brain
11	chr7:71615400-71619000	Enhancers	Pancreas	Pancrea
12	chr7:71615400-71619600	Enhancers	Brain Angular Gyrus	brain
13	chr7:71615800-71616200	Enhancers	H9 Cell Line	embryonic stem cell
14	chr7:71615800-71616200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr7:71615800-71616800	ZNF genes & repeats	Dnd41	blood

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