Variant report

Variant	rs62172429
Chromosome Location	chr2:188416472-188416473
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:188413943-188416995	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr2:188413653-188416610	HUVEC	blood vessel:	n/a	n/a
3	MBD4	chr2:188410002-188416722	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:188415454-188416556	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:188410665-188416978	K562	blood:	n/a	n/a
6	POLR2A	chr2:188415527-188416561	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr2:188412875-188416718	HepG2	liver:	n/a	n/a
8	ARID3A	chr2:188416243-188416679	K562	blood:	n/a	n/a
9	IRF1	chr2:188416468-188416668	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:188395046..188397968-chr2:188414786..188417959,4	K562	blood:
2	chr2:188350155..188352503-chr2:188415198..188418799,3	K562	blood:
3	chr2:188415101..188417280-chr2:188445536..188447377,2	K562	blood:
4	chr2:188412314..188413944-chr2:188414421..188417624,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000224063	TF binding region

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

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

rs_ID	r²[population]
rs10164687	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10209536	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11904140	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12465456	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12469935	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12474650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431970	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666730	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666731	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667177	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667179	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58172383	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59650207	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60883561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172428	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172435	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172453	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172454	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172455	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172456	1.00[ASN][1000 genomes]
rs62172457	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62172459	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62174260	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72906235	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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	nsv875561	chr2:188226900-188440752	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv875565	chr2:188258904-188440752	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188398400-188418000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:188406200-188418600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:188406800-188417200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:188406800-188418000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:188406800-188418600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:188406800-188422800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:188410800-188417800	Weak transcription	Fetal Kidney	kidney
8	chr2:188410800-188420600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:188411000-188418800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:188411200-188419000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:188412600-188417600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:188412600-188418200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:188412600-188418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:188413200-188417200	Weak transcription	Fetal Stomach	stomach
15	chr2:188413200-188417400	Enhancers	Stomach Mucosa	stomach
16	chr2:188413400-188417800	Weak transcription	HMEC	breast
17	chr2:188413400-188417800	Weak transcription	NHEK	skin
18	chr2:188413400-188418800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:188413600-188419800	Active TSS	Right Atrium	heart
20	chr2:188413800-188417800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:188414000-188416600	Flanking Active TSS	HUVEC	blood vessel
22	chr2:188414000-188416800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr2:188414000-188417200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:188414200-188417400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:188414400-188416600	Flanking Active TSS	HepG2	liver
26	chr2:188414600-188416600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:188414600-188417800	Enhancers	Fetal Intestine Small	intestine
28	chr2:188414600-188419600	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr2:188415000-188416800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:188415000-188417200	Enhancers	Fetal Intestine Large	intestine
31	chr2:188415000-188417800	Weak transcription	Fetal Brain Male	brain
32	chr2:188415000-188431200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr2:188415200-188416600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
34	chr2:188415600-188416800	Enhancers	Primary hematopoietic stem cells	blood
35	chr2:188415600-188417000	Flanking Active TSS	NHDF-Ad	bronchial
36	chr2:188415600-188417200	Enhancers	Dnd41	blood
37	chr2:188415600-188419400	Active TSS	Adipose Nuclei	Adipose
38	chr2:188415800-188416600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:188415800-188417600	Weak transcription	Placenta	Placenta
40	chr2:188415800-188419600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:188416000-188416600	Flanking Active TSS	Hela-S3	cervix
42	chr2:188416000-188420400	Active TSS	Duodenum Mucosa	Duodenum
43	chr2:188416200-188417800	Weak transcription	Ovary	ovary
44	chr2:188416200-188418200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:188416200-188419800	Active TSS	HSMMtube	muscle
46	chr2:188416400-188416600	Flanking Active TSS	NH-A	brain
47	chr2:188416400-188416800	Enhancers	Osteobl	bone
48	chr2:188416400-188417000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:188416400-188417200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:188416400-188417200	Weak transcription	Right Ventricle	heart

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