Variant report

Variant	rs6965740
Chromosome Location	chr7:117514840-117514841
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:115890993-115892266..7:117514740-117523593	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
ENSG00000135269	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10233018	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10242758	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10272923	0.95[JPT][hapmap]
rs10953856	0.93[ASW][hapmap];0.82[YRI][hapmap]
rs1156954	0.95[JPT][hapmap]
rs11978052	0.95[JPT][hapmap]
rs12154872	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13221302	0.95[JPT][hapmap]
rs1548460	0.95[JPT][hapmap];0.81[TSI][hapmap]
rs1548461	0.81[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs17488728	0.94[JPT][hapmap]
rs1989880	0.95[JPT][hapmap]
rs2193255	0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35895632	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6943120	0.95[JPT][hapmap]
rs6950622	0.91[JPT][hapmap]
rs6959314	0.95[JPT][hapmap]
rs6966339	0.95[JPT][hapmap];0.81[TSI][hapmap]
rs6969783	0.95[JPT][hapmap]
rs7796203	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7807019	0.95[JPT][hapmap]
rs7807677	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7809993	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6965740	CCS	trans	parietal	SCAN
rs6965740	TTL	trans	parietal	SCAN
rs6965740	CTSZ	trans	parietal	SCAN
rs6965740	GPX7	trans	parietal	SCAN
rs6965740	WNT2	cis	cerebellum	SCAN
rs6965740	C7orf58	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117514000-117515600	Weak transcription	Esophagus	oesophagus
2	chr7:117514000-117516400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:117514000-117524000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:117514200-117515200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:117514200-117515600	Weak transcription	Fetal Stomach	stomach
6	chr7:117514400-117515000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
7	chr7:117514400-117515000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
8	chr7:117514400-117515400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr7:117514400-117515600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr7:117514400-117516400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:117514400-117516400	Weak transcription	Brain Hippocampus Middle	brain
12	chr7:117514400-117516600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr7:117514600-117515200	Weak transcription	Fetal Brain Female	brain
14	chr7:117514600-117515600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr7:117514600-117515600	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr7:117514600-117515600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr7:117514600-117515600	Weak transcription	Adipose Nuclei	Adipose
18	chr7:117514600-117515600	Weak transcription	NHLF	lung
19	chr7:117514600-117515800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:117514600-117517200	Enhancers	Fetal Brain Male	brain
21	chr7:117514800-117515000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr7:117514800-117515600	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr7:117514800-117516400	Weak transcription	H9 Cell Line	embryonic stem cell

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