Variant report

Variant	rs3789687
Chromosome Location	chr1:94693703-94693704
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94693083..94695209-chr1:94701584..94703988,3	MCF-7	breast:
2	chr1:94692312..94694422-chr1:94696835..94699203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137962	Chromatin interaction

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];0.96[ASN][1000 genomes]
rs10443184	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs1048866	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs10782980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874840	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11165090	0.83[EUR][1000 genomes]
rs11165099	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11165101	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11165108	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165110	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11196	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs12750249	0.97[ASN][1000 genomes]
rs1411698	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs1411700	0.83[EUR][1000 genomes]
rs1411701	0.83[EUR][1000 genomes]
rs1687935	0.93[ASN][1000 genomes]
rs1756245	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1756248	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1929130	0.84[EUR][1000 genomes]
rs2077424	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2210161	0.93[ASN][1000 genomes]
rs35791244	0.88[EUR][1000 genomes]
rs3814020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6541340	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6541411	0.84[EUR][1000 genomes]
rs6697764	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67070250	1.00[ASN][1000 genomes]
rs7536759	0.87[EUR][1000 genomes]
rs7540185	0.83[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3789687	NENF	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94668800-94699000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:94673800-94698600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr1:94673800-94701000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:94674000-94697000	Weak transcription	HSMMtube	muscle
5	chr1:94684800-94698600	Weak transcription	Left Ventricle	heart
6	chr1:94685000-94701000	Weak transcription	Right Ventricle	heart
7	chr1:94685200-94696800	Weak transcription	HepG2	liver
8	chr1:94685200-94700600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:94685200-94700800	Weak transcription	NHLF	lung
10	chr1:94685200-94701000	Weak transcription	Psoas Muscle	Psoas
11	chr1:94685400-94697400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:94685600-94696000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr1:94685800-94693800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:94685800-94699400	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:94688000-94694600	Weak transcription	HMEC	breast
16	chr1:94688200-94694200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:94688400-94694400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:94688600-94694600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:94690400-94696400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:94691400-94693800	Enhancers	Liver	Liver
21	chr1:94691600-94696200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:94691600-94696400	Weak transcription	HSMM	muscle
23	chr1:94692200-94694000	Weak transcription	NHEK	skin
24	chr1:94692200-94694400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:94692200-94696600	Weak transcription	NH-A	brain
26	chr1:94692400-94694400	Weak transcription	NHDF-Ad	bronchial
27	chr1:94692600-94694200	Genic enhancers	Muscle Satellite Cultured Cells	--
28	chr1:94692600-94694400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:94692600-94695600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:94692600-94700200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:94693200-94695200	Enhancers	Osteobl	bone
32	chr1:94693400-94693800	Weak transcription	A549	lung
33	chr1:94693400-94694200	Weak transcription	Adipose Nuclei	Adipose
34	chr1:94693400-94695200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:94693400-94696400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr1:94693600-94694000	Weak transcription	Fetal Heart	heart
37	chr1:94693600-94696800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:94693600-94697000	Enhancers	HUVEC	blood vessel

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