Variant report

Variant	rs2351419
Chromosome Location	chr2:189835057-189835058
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	CEBPB	chr2:189834976-189835579	IMR90	lung:	n/a	chr2:189835050-189835063
2	GATA3	chr2:189834820-189835361	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
COL3A1	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11887092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11894810	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894811	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11900672	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12469508	0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12470993	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12472287	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12472298	1.00[ASN][1000 genomes]
rs12472852	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12476698	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12477499	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12619321	1.00[CEU][hapmap]
rs13026408	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16830936	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16830939	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16830965	1.00[CEU][hapmap]
rs2138536	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3806465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41265571	0.95[ASN][1000 genomes]
rs6720645	0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6752174	0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7568165	1.00[CEU][hapmap]
rs7579124	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834490	chr2:189703550-189840963	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv875608	chr2:189753823-189837995	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv1849974	chr2:189796272-189837995	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv584056	chr2:189796272-189841052	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv459992	chr2:189796272-189855943	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv584057	chr2:189796272-189855943	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv875609	chr2:189796272-189862097	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv875610	chr2:189796272-189904674	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv875611	chr2:189799499-189837212	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv584058	chr2:189799499-189855943	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
11	esv1791841	chr2:189811074-189864582	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189828400-189838400	Weak transcription	Fetal Kidney	kidney
2	chr2:189830800-189839000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr2:189831800-189836000	Weak transcription	Ovary	ovary
4	chr2:189832600-189836400	Enhancers	Colon Smooth Muscle	Colon
5	chr2:189833600-189835200	Enhancers	Rectal Smooth Muscle	rectum
6	chr2:189833600-189836400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:189833600-189836400	Enhancers	HSMMtube	muscle
8	chr2:189833600-189836600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:189833600-189836600	Enhancers	Osteobl	bone
10	chr2:189833600-189836800	Enhancers	Fetal Lung	lung
11	chr2:189834000-189835600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:189834200-189838600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:189834200-189838800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:189834200-189842800	Weak transcription	A549	lung
15	chr2:189834400-189835200	Flanking Active TSS	NHDF-Ad	bronchial
16	chr2:189834400-189836400	Enhancers	NHLF	lung
17	chr2:189834400-189838200	Weak transcription	Fetal Muscle Leg	muscle
18	chr2:189834800-189835200	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr2:189834800-189835200	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr2:189834800-189835200	Enhancers	HSMM	muscle
21	chr2:189834800-189837200	Enhancers	Adipose Nuclei	Adipose
22	chr2:189835000-189835200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:189835000-189835200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:189835000-189835200	Enhancers	Fetal Stomach	stomach
25	chr2:189835000-189835400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:189835000-189835400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:189835000-189835800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:189835000-189836800	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links