Variant report

Variant	rs3814019
Chromosome Location	chr1:94704396-94704397
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	chr1:94700194-94705855	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr1:94701676-94704719	HCT-116	colon:	n/a	n/a
3	POLR2A	chr1:94702834-94704582	HCT-116	colon:	n/a	n/a
4	POLR2A	chr1:94700765-94705191	PANC-1	pancreas:	n/a	n/a

Variant related genes	Relation type
ARHGAP29	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11165098	0.94[ASN][1000 genomes]
rs11165104	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11165105	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11165111	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11165120	0.88[YRI][hapmap]
rs11587699	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12069420	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12084043	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12090310	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12090491	0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12096115	0.84[ASN][1000 genomes]
rs1330855	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1687949	0.98[ASN][1000 genomes]
rs17111360	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1756254	0.94[ASN][1000 genomes]
rs2150269	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2774923	0.96[ASN][1000 genomes]
rs28613199	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs35493159	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789688	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[YRI][hapmap];0.93[ASN][1000 genomes]
rs3827751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58466782	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs59960594	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs722296	0.91[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7525008	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7528831	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7530160	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7535547	0.88[YRI][hapmap]
rs7538484	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540684	0.98[ASN][1000 genomes]
rs7548951	0.83[AFR][1000 genomes];0.95[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	esv3326788	chr1:94701989-94704537	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3814019	BARHL2	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94703200-94706400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:94703600-94704800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:94703600-94705400	Enhancers	Muscle Satellite Cultured Cells	--
4	chr1:94703600-94705800	Enhancers	HMEC	breast
5	chr1:94703600-94709000	Enhancers	HUVEC	blood vessel
6	chr1:94703600-94712000	Weak transcription	HSMM	muscle
7	chr1:94703800-94704400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:94703800-94704600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:94703800-94704800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:94703800-94704800	Enhancers	Psoas Muscle	Psoas
11	chr1:94703800-94705400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:94703800-94705800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:94703800-94705800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:94704000-94704400	Bivalent Enhancer	Primary T cells from cord blood	blood
15	chr1:94704000-94705800	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:94704000-94709000	Weak transcription	Liver	Liver
17	chr1:94704200-94704600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:94704200-94704800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:94704200-94705000	Weak transcription	A549	lung
20	chr1:94704200-94705000	Weak transcription	NHDF-Ad	bronchial
21	chr1:94704200-94705400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:94704200-94705400	Weak transcription	NH-A	brain
23	chr1:94704200-94705600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:94704200-94705600	Weak transcription	Left Ventricle	heart
25	chr1:94704200-94705800	Enhancers	NHEK	skin
26	chr1:94704200-94706000	Enhancers	Osteobl	bone
27	chr1:94704200-94706200	Weak transcription	HepG2	liver

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