Variant report

Variant	rs7512365
Chromosome Location	chr1:216995679-216995680
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1030846	0.84[CEU][hapmap];0.83[CHB][hapmap];0.90[GIH][hapmap];0.88[LWK][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1126022	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12745662	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1339337	0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1339338	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1339348	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1339356	0.88[CEU][hapmap];0.83[CHB][hapmap];0.90[GIH][hapmap];0.88[LWK][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1344873	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1436888	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1832532	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2032028	0.83[ASW][hapmap];0.88[CEU][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2118151	0.81[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2576234	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576235	0.83[CEU][hapmap]
rs2576236	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2576238	0.96[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2789716	0.84[CEU][hapmap];0.83[CHB][hapmap];0.90[GIH][hapmap];0.88[LWK][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2789720	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2813671	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2813674	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4575149	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6604647	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7554036	0.87[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][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	esv2762163	chr1:216982140-217015625	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7512365	C1orf97	cis	parietal	SCAN
rs7512365	MT3	trans	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216988000-216997200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:216989000-217005800	Weak transcription	Left Ventricle	heart
3	chr1:216989400-216998200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:216989600-216997800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:216989600-216998000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:216989600-217000600	Weak transcription	Psoas Muscle	Psoas
7	chr1:216990000-216998000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:216992400-216996800	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr1:216993200-216995800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:216994200-216996000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:216994200-216998000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:216994400-216998200	Weak transcription	Small Intestine	intestine
13	chr1:216994600-216996400	Weak transcription	Fetal Intestine Small	intestine
14	chr1:216994600-216997000	Weak transcription	Fetal Intestine Large	intestine
15	chr1:216994600-217004000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:216994800-216998600	Weak transcription	Fetal Heart	heart
17	chr1:216995400-216997200	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr1:216995600-216995800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:216995600-216996600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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