Variant report

Variant	rs10913672
Chromosome Location	chr1:178981416-178981417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:178973042..178975916-chr1:178979965..178981961,3	K562	blood:
2	chr1:178975112..178978831-chr1:178980259..178984628,4	MCF-7	breast:
3	chr1:178978287..178981942-chr1:178982197..178988679,6	K562	blood:
4	chr1:178979785..178981942-chr1:178983318..178985358,3	K562	blood:
5	chr1:178980100..178983059-chr1:178999156..179001335,2	K562	blood:
6	chr1:178981145..178983192-chr1:178997172..178999503,2	K562	blood:
7	chr1:178974332..178978304-chr1:178979195..178983919,4	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10082052	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1046385	1.00[ASW][hapmap];0.83[GIH][hapmap];0.80[TSI][hapmap]
rs1325194	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs2025582	1.00[LWK][hapmap]
rs2182102	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2296377	0.82[GIH][hapmap]
rs2636290	1.00[ASW][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap]
rs3813638	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3818433	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs4360489	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4652344	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4652348	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6425512	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425515	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs6697029	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7532578	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7538498	1.00[CEU][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7544801	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[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	nsv548275	chr1:178978409-178985658	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10913672	ABL2	cis	parietal	SCAN
rs10913672	GPR52	cis	parietal	SCAN
rs10913672	FAM20B	cis	parietal	SCAN
rs10913672	RALGPS2	cis	parietal	SCAN
rs10913672	TOR3A	cis	multi-tissue	Pritchard
rs10913672	FAM20B	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:178972400-178986000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:178973600-178983200	Weak transcription	K562	blood
3	chr1:178977000-178985400	Weak transcription	A549	lung
4	chr1:178977000-178985600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:178977200-178981600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:178978200-178984600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:178978200-178986000	Weak transcription	HepG2	liver
8	chr1:178978600-178986000	Weak transcription	Right Atrium	heart
9	chr1:178978600-178991000	Weak transcription	Aorta	Aorta
10	chr1:178978600-178991200	Weak transcription	Psoas Muscle	Psoas
11	chr1:178979800-178981800	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr1:178980400-178985600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:178980800-178982200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:178981000-178981800	Enhancers	Stomach Smooth Muscle	stomach
15	chr1:178981200-178981600	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr1:178981200-178981800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:178981200-178981800	Enhancers	Adipose Nuclei	Adipose
18	chr1:178981200-178981800	Enhancers	Fetal Intestine Small	intestine
19	chr1:178981400-178981600	Enhancers	Stomach Mucosa	stomach
20	chr1:178981400-178981800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:178981400-178981800	Enhancers	Skeletal Muscle Female	skeletal muscle

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