Variant report

Variant	rs62172459
Chromosome Location	chr2:188441229-188441230
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:188433750..188436567-chr2:188440064..188442739,2	K562	blood:
2	chr2:188440243..188443082-chr2:188444632..188448024,3	K562	blood:
3	chr2:188440946..188443688-chr2:188443875..188445768,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10164687	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209536	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11904140	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465456	1.00[ASN][1000 genomes]
rs12469935	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12474650	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431970	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666730	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666731	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4667177	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667179	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58172383	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59650207	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60883561	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172428	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172429	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172435	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172436	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172453	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172455	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172456	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172457	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62174260	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72906235	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875560	chr2:188219052-188508011	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv875566	chr2:188258904-188626214	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv875567	chr2:188258904-188673462	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv875568	chr2:188291105-188653806	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv875576	chr2:188343497-188482933	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv875577	chr2:188343497-188500930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv875578	chr2:188343497-188690187	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv997899	chr2:188356689-188531831	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1014298	chr2:188359747-188531831	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1013166	chr2:188359747-188544803	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1014942	chr2:188360116-188480738	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv584038	chr2:188370232-188450136	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv875580	chr2:188370232-188521234	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	esv2757845	chr2:188380042-188503185	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	esv2759108	chr2:188380042-188503185	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv875581	chr2:188390819-188521234	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv875582	chr2:188395700-188508011	Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv875583	chr2:188395700-188521234	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv875584	chr2:188414161-188500930	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv875585	chr2:188424525-188626214	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
21	nsv584039	chr2:188435643-188482933	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188419400-188445400	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:188439400-188442400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:188439600-188442200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:188439600-188442400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr2:188439600-188442400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr2:188439600-188442400	Enhancers	Hela-S3	cervix
7	chr2:188439600-188442400	Enhancers	HepG2	liver
8	chr2:188439600-188442600	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr2:188439800-188441400	Weak transcription	Fetal Intestine Large	intestine
10	chr2:188439800-188442600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr2:188440000-188445600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr2:188440200-188445200	Weak transcription	NH-A	brain
13	chr2:188440400-188441600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:188440400-188441600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:188440400-188441600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr2:188440400-188442400	Enhancers	A549	lung
17	chr2:188440400-188445200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:188440400-188445200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:188440400-188445200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:188440400-188445600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:188440600-188445200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:188440600-188445200	Weak transcription	Adipose Nuclei	Adipose
23	chr2:188440600-188445600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:188440600-188445600	Weak transcription	HSMM	muscle
25	chr2:188440800-188441400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:188440800-188441600	Weak transcription	Liver	Liver
27	chr2:188440800-188441600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr2:188440800-188441600	Weak transcription	Stomach Mucosa	stomach
29	chr2:188440800-188442000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:188440800-188442200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:188440800-188442400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:188440800-188442400	Enhancers	HUVEC	blood vessel
33	chr2:188440800-188444800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:188440800-188445200	Weak transcription	NHDF-Ad	bronchial
35	chr2:188440800-188445600	Weak transcription	Fetal Kidney	kidney
36	chr2:188441000-188441400	Weak transcription	Fetal Lung	lung
37	chr2:188441000-188441600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:188441000-188441600	Weak transcription	Fetal Intestine Small	intestine
39	chr2:188441000-188441800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:188441000-188441800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:188441000-188442000	Weak transcription	Osteobl	bone
42	chr2:188441000-188445000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:188441000-188445200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr2:188441000-188445200	Weak transcription	Small Intestine	intestine
45	chr2:188441000-188445200	Weak transcription	NHLF	lung
46	chr2:188441000-188445600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr2:188441200-188441600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:188441200-188441600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:188441200-188441600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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