Variant report

Variant	rs3814020
Chromosome Location	chr1:94704630-94704631
allele	A/G/T
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	SPI1	chr1:94704608-94705044	HL-60	blood:	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: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10158261	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10443184	0.83[EUR][1000 genomes]
rs1048866	0.81[EUR][1000 genomes]
rs10782980	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10874840	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11165090	0.81[EUR][1000 genomes]
rs11165099	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11165101	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11165108	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11165110	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11196	0.81[EUR][1000 genomes]
rs12750249	0.98[ASN][1000 genomes]
rs1411698	0.83[EUR][1000 genomes]
rs1411700	0.81[EUR][1000 genomes]
rs1411701	0.81[EUR][1000 genomes]
rs1687935	0.94[ASN][1000 genomes]
rs1756245	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1756248	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1929130	0.82[EUR][1000 genomes]
rs2077424	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2210161	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35791244	0.86[EUR][1000 genomes]
rs3789687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6541340	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6541411	0.84[EUR][1000 genomes]
rs6697764	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67070250	0.99[ASN][1000 genomes]
rs7536759	0.85[EUR][1000 genomes]
rs7540185	0.84[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3814020	NENF	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 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	chr1:94703800-94704800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:94703800-94704800	Enhancers	Psoas Muscle	Psoas
9	chr1:94703800-94705400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:94703800-94705800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:94703800-94705800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:94704000-94705800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr1:94704000-94709000	Weak transcription	Liver	Liver
14	chr1:94704200-94704800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:94704200-94705000	Weak transcription	A549	lung
16	chr1:94704200-94705000	Weak transcription	NHDF-Ad	bronchial
17	chr1:94704200-94705400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:94704200-94705400	Weak transcription	NH-A	brain
19	chr1:94704200-94705600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:94704200-94705600	Weak transcription	Left Ventricle	heart
21	chr1:94704200-94705800	Enhancers	NHEK	skin
22	chr1:94704200-94706000	Enhancers	Osteobl	bone
23	chr1:94704200-94706200	Weak transcription	HepG2	liver
24	chr1:94704600-94704800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
25	chr1:94704600-94704800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:94704600-94704800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:94704600-94705000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
28	chr1:94704600-94705000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
29	chr1:94704600-94705200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:94704600-94705800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:94704600-94705800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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