Variant report

Variant	rs1903109
Chromosome Location	chr4:119903439-119903440
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:119902678..119903605-chr4:120207219..120207879,4	K562	blood:
2	chr4:119903318..119905119-chr4:120133808..120135717,2	MCF-7	breast:
3	chr4:119902777..119905378-chr4:119907189..119909991,2	MCF-7	breast:
4	chr4:119902691..119903668-chr4:119960868..119961628,4	MCF-7	breast:
5	chr17:27717127..27719243-chr4:119902588..119905576,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160551	Chromatin interaction
ENSG00000264808	Chromatin interaction
ENSG00000263719	Chromatin interaction
ENSG00000145390	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10434027	0.92[AFR][1000 genomes]
rs12642839	0.82[ASN][1000 genomes]
rs12644954	0.82[ASN][1000 genomes]
rs12711068	0.80[ASN][1000 genomes]
rs13102598	0.82[ASN][1000 genomes]
rs13103225	0.82[ASN][1000 genomes]
rs28397961	0.82[ASN][1000 genomes]
rs59089242	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9307465	0.84[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1903109	BBS7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119896400-119907600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:119896800-119903600	Weak transcription	Right Ventricle	heart
3	chr4:119901400-119905400	Enhancers	Ovary	ovary
4	chr4:119901400-119907000	Enhancers	Psoas Muscle	Psoas
5	chr4:119901400-119911600	Enhancers	Rectal Smooth Muscle	rectum
6	chr4:119901600-119903800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:119901600-119904600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:119901600-119904600	Enhancers	Osteobl	bone
9	chr4:119901800-119904200	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr4:119902000-119904000	Enhancers	Fetal Heart	heart
11	chr4:119902000-119904400	Enhancers	HSMMtube	muscle
12	chr4:119902000-119904600	Enhancers	NHDF-Ad	bronchial
13	chr4:119902000-119904800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:119902000-119904800	Enhancers	NH-A	brain
15	chr4:119902200-119903600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr4:119902200-119904200	Enhancers	NHLF	lung
17	chr4:119902200-119904600	Enhancers	HSMM	muscle
18	chr4:119902200-119905800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:119902200-119906400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr4:119902600-119903600	Enhancers	Brain Anterior Caudate	brain
21	chr4:119902600-119907000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:119902800-119904000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr4:119902800-119904600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:119903000-119903600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr4:119903000-119905600	Weak transcription	Fetal Muscle Leg	muscle
26	chr4:119903000-119909800	Weak transcription	Fetal Stomach	stomach
27	chr4:119903000-119910200	Enhancers	Colon Smooth Muscle	Colon
28	chr4:119903200-119903600	Enhancers	Adipose Nuclei	Adipose
29	chr4:119903200-119903600	Weak transcription	Aorta	Aorta
30	chr4:119903200-119903600	Weak transcription	Left Ventricle	heart
31	chr4:119903200-119903600	Weak transcription	Right Atrium	heart
32	chr4:119903200-119903600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr4:119903200-119903800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:119903200-119904800	Enhancers	HMEC	breast
35	chr4:119903400-119903800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:119903400-119903800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr4:119903400-119904000	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr4:119903400-119904200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:119903400-119904400	Weak transcription	Monocytes-CD14+_RO01746	blood

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