Variant report

Variant	rs6594050
Chromosome Location	chr2:110375151-110375152
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:110369085-110379088	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr2:110375025-110375355	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:110375065-110375312	Hela-S3	cervix:	n/a	n/a
4	HEY1	chr2:110374989-110375351	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:110374617-110375300	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:110369290-110378742	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr2:110374122-110375164	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr2:110375003-110375380	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr2:110374989-110375382	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:110373614..110376215-chr2:110402569..110405240,2	MCF-7	breast:
2	chr2:110373452..110379192-chr2:110379492..110383330,5	MCF-7	breast:

Variant related genes	Relation type
SEPT10	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1036317	0.84[EUR][1000 genomes]
rs1036318	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10496432	0.94[ASW][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1811388	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28441405	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28445980	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28570680	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs28612440	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28696274	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28719680	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3213866	0.88[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34111852	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34311530	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34441132	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34517320	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs34821058	0.94[ASW][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35120088	0.83[AMR][1000 genomes]
rs35223862	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35392016	0.83[AMR][1000 genomes]
rs35550721	0.85[EUR][1000 genomes]
rs35955221	0.83[AMR][1000 genomes]
rs4482487	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4953729	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4953730	0.88[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs4953788	0.88[ASW][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4953847	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953853	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55794045	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56265736	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56794190	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs58031484	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6594053	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6594054	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6709945	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6719215	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6725792	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6737736	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751785	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6760577	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72824788	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72824796	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72824802	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72826816	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72826817	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs753492	0.88[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7565483	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7577865	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs892462	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9330317	0.83[AMR][1000 genomes]
rs9330321	0.83[AMR][1000 genomes]
rs9752531	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9798179	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1009367	chr2:110349178-110863354	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv829617	chr2:110359857-110380012	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
8	esv2762780	chr2:110367969-110462496	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6594050	ACOXL	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110373000-110375800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:110373200-110375400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:110373600-110375200	Weak transcription	Lung	lung
4	chr2:110373800-110375200	Flanking Active TSS	Liver	Liver
5	chr2:110374000-110375200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:110374000-110375200	Weak transcription	Esophagus	oesophagus
7	chr2:110374000-110377200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:110374000-110378000	Weak transcription	HSMM	muscle
9	chr2:110374000-110379200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:110374200-110375200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:110374200-110376600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:110374200-110376800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:110374200-110377200	Enhancers	Fetal Intestine Small	intestine
14	chr2:110374200-110377800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr2:110374200-110377800	Enhancers	Fetal Intestine Large	intestine
16	chr2:110374200-110377800	Weak transcription	NHDF-Ad	bronchial
17	chr2:110374400-110375200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:110374400-110375200	Active TSS	A549	lung
19	chr2:110374600-110375800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:110374600-110376800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:110374600-110377000	Weak transcription	GM12878-XiMat	blood
22	chr2:110374600-110377800	Weak transcription	Fetal Lung	lung
23	chr2:110374600-110378000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:110374600-110380000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:110374800-110375200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:110374800-110375200	Enhancers	Adipose Nuclei	Adipose
27	chr2:110374800-110375200	Enhancers	Fetal Brain Male	brain
28	chr2:110374800-110375200	Active TSS	HMEC	breast
29	chr2:110374800-110375400	Enhancers	Brain Germinal Matrix	brain
30	chr2:110374800-110375600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:110375000-110375200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:110375000-110375200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr2:110375000-110375200	Enhancers	Pancreas	Pancrea
34	chr2:110375000-110375400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:110375000-110375400	Flanking Active TSS	Hela-S3	cervix
36	chr2:110375000-110375400	Flanking Active TSS	HepG2	liver
37	chr2:110375000-110375400	Flanking Active TSS	NHEK	skin
38	chr2:110375000-110376800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:110375000-110377600	Weak transcription	Rectal Smooth Muscle	rectum

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