Variant report

Variant	rs1878199
Chromosome Location	chr2:189831353-189831354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1040186	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1122869	0.87[EUR][1000 genomes]
rs12618257	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12693520	0.84[ASN][1000 genomes]
rs12693522	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12693523	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs12693524	1.00[ASN][1000 genomes]
rs12990937	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1516443	0.88[ASN][1000 genomes]
rs1878200	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs2138533	0.82[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2351418	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4667254	0.84[ASN][1000 genomes]
rs6434304	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6434305	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7568409	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1008398	chr2:189794993-189831353	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189828400-189838400	Weak transcription	Fetal Kidney	kidney
2	chr2:189829000-189833600	Weak transcription	Fetal Stomach	stomach
3	chr2:189829200-189833600	Weak transcription	NHLF	lung
4	chr2:189830400-189832000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:189830600-189831600	Weak transcription	Aorta	Aorta
6	chr2:189830600-189832000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:189830600-189832200	Enhancers	Adipose Nuclei	Adipose
8	chr2:189830800-189831400	Enhancers	Colon Smooth Muscle	Colon
9	chr2:189830800-189832000	Enhancers	Muscle Satellite Cultured Cells	--
10	chr2:189830800-189832000	Enhancers	Rectal Smooth Muscle	rectum
11	chr2:189830800-189833600	Enhancers	NHDF-Ad	bronchial
12	chr2:189830800-189839000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:189831200-189831600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:189831200-189831600	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:189831200-189831600	Weak transcription	Ovary	ovary
16	chr2:189831200-189831800	Enhancers	Fetal Lung	lung
17	chr2:189831200-189834800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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dbSNP/dbVar ID: rs12345 /nsv7879
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