Variant report

Variant	rs28690965
Chromosome Location	chr4:120034317-120034318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:119989699..119991632-chr4:120032879..120034725,2	MCF-7	breast:
2	chr4:120033457..120035928-chr4:120042450..120044760,2	MCF-7	breast:
3	chr4:120033922..120036234-chr4:120037431..120039972,2	K562	blood:
4	chr4:120032730..120035461-chr4:120133316..120136122,2	MCF-7	breast:
5	chr4:120033091..120034925-chr4:120132885..120135454,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249356	Chromatin interaction
ENSG00000178636	Chromatin interaction
ENSG00000145390	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10029388	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10031010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12650325	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1809263	0.87[ASN][1000 genomes]
rs1809264	0.91[ASN][1000 genomes]
rs28455602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28523531	0.91[ASN][1000 genomes]
rs28580586	0.91[ASN][1000 genomes]
rs4834749	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61391192	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62326879	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1007214	chr4:120007913-120112460	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1008115	chr4:120007913-120143849	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
5	nsv1003827	chr4:120008227-120112460	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv522386	chr4:120009147-120115379	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
8	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
9	nsv1007619	chr4:120014898-120112460	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28690965	FABP2	cis	Whole Blood	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120014800-120045000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:120024600-120036800	Weak transcription	Right Ventricle	heart
3	chr4:120027800-120034600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:120028200-120034600	Weak transcription	HSMMtube	muscle
5	chr4:120028200-120038000	Weak transcription	Left Ventricle	heart
6	chr4:120028200-120038200	Weak transcription	Aorta	Aorta
7	chr4:120030800-120035400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:120033400-120034400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:120033400-120035400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr4:120033600-120034600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:120033600-120035000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:120033600-120035200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:120033600-120035400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr4:120033600-120035400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:120033800-120035400	Enhancers	NHEK	skin
16	chr4:120034000-120034600	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr4:120034000-120034800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:120034000-120034800	Enhancers	Adipose Nuclei	Adipose
19	chr4:120034000-120035000	Enhancers	Primary hematopoietic stem cells	blood
20	chr4:120034000-120035000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:120034000-120035000	Enhancers	A549	lung
22	chr4:120034000-120035000	Enhancers	Hela-S3	cervix
23	chr4:120034000-120035000	Enhancers	NHLF	lung
24	chr4:120034000-120035200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr4:120034000-120035200	Enhancers	NH-A	brain
26	chr4:120034000-120035200	Enhancers	Osteobl	bone
27	chr4:120034000-120035400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr4:120034000-120035400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:120034000-120035400	Enhancers	HMEC	breast
30	chr4:120034000-120035400	Enhancers	HSMM	muscle
31	chr4:120034000-120035400	Enhancers	NHDF-Ad	bronchial
32	chr4:120034200-120034400	Flanking Active TSS	HUVEC	blood vessel
33	chr4:120034200-120034600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:120034200-120034800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:120034200-120034800	Enhancers	Dnd41	blood
36	chr4:120034200-120035000	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr4:120034200-120035400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links