Variant report

Variant	rs12700617
Chromosome Location	chr7:25389745-25389746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1002203	0.87[EUR][1000 genomes]
rs1015497	0.86[EUR][1000 genomes]
rs10807824	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11764103	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11769627	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11972231	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11981869	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12670448	0.81[ASN][1000 genomes]
rs12672062	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12672230	0.93[ASN][1000 genomes]
rs12700607	0.93[ASN][1000 genomes]
rs12700608	0.93[ASN][1000 genomes]
rs12700609	0.93[ASN][1000 genomes]
rs12700610	0.81[ASN][1000 genomes]
rs12700611	0.93[ASN][1000 genomes]
rs12700612	0.93[ASN][1000 genomes]
rs12700613	0.93[ASN][1000 genomes]
rs12700614	0.93[ASN][1000 genomes]
rs12700616	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12700618	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700619	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12700620	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700621	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700623	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12700624	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12700625	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12700628	0.87[EUR][1000 genomes]
rs13221394	0.87[EUR][1000 genomes]
rs13310680	0.92[EUR][1000 genomes]
rs1988282	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1988283	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2188993	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4134095	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6461862	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6461864	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6953741	0.81[EUR][1000 genomes]
rs6964890	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7811651	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs929239	0.88[EUR][1000 genomes]
rs929240	0.88[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	nsv606424	chr7:24982529-25466521	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv606426	chr7:25254125-25621579	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv887846	chr7:25371700-25407621	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12700617	CDCA7L	cis	parietal	SCAN
rs12700617	CPVL	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25386400-25390000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:25389200-25390000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:25389400-25390200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:25389400-25391200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr7:25389400-25391200	Weak transcription	Small Intestine	intestine
6	chr7:25389600-25389800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr7:25389600-25391200	Weak transcription	Fetal Intestine Large	intestine
8	chr7:25389600-25391200	Weak transcription	Rectal Mucosa Donor 31	rectum

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