Variant report

Variant	rs13411086
Chromosome Location	chr2:188415501-188415502
allele	C/T
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	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	MAZ	chr2:188415352-188415531	HepG2	liver:	n/a	n/a
4	TEAD4	chr2:188414487-188415784	HepG2	liver:	n/a	n/a
5	MBD4	chr2:188410002-188416722	HepG2	liver:	n/a	n/a
6	POLR2A	chr2:188415454-188416556	HepG2	liver:	n/a	n/a
7	HEY1	chr2:188414297-188416436	HepG2	liver:	n/a	n/a
8	MYBL2	chr2:188413852-188416295	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:188410665-188416978	K562	blood:	n/a	n/a
10	POLR2A	chr2:188412875-188416718	HepG2	liver:	n/a	n/a
11	ARID3A	chr2:188414692-188415523	HepG2	liver:	n/a	n/a
12	MBD4	chr2:188414501-188416438	HepG2	liver:	n/a	n/a
13	GATA1	chr2:188415395-188416437	PBDE	blood:	n/a	chr2:188415666-188415687 chr2:188415671-188415680 chr2:188415673-188415680 chr2:188415668-188415684 chr2:188415669-188415682
14	NFIC	chr2:188413801-188416267	HepG2	liver:	n/a	chr2:188414032-188414060

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:

Variant related genes	Relation type
ENSG00000224063	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10153820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10177003	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10185334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10191373	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11902917	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13425112	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13427829	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4366866	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4643503	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4666732	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4666734	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4667168	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56141195	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56170850	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60452662	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6434222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6434223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6715871	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6749781	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756052	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73052654	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73052656	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73982974	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9288142	0.97[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:75 , 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	chr2:188406800-188415600	Weak transcription	Spleen	Spleen
4	chr2:188406800-188417200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:188406800-188418000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr2:188406800-188418600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:188406800-188422800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:188409800-188415600	Weak transcription	Placenta	Placenta
9	chr2:188409800-188415600	Weak transcription	Lung	lung
10	chr2:188409800-188415600	Weak transcription	Ovary	ovary
11	chr2:188409800-188416000	Weak transcription	Left Ventricle	heart
12	chr2:188410800-188417800	Weak transcription	Fetal Kidney	kidney
13	chr2:188410800-188420600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:188411000-188416200	Enhancers	Fetal Lung	lung
15	chr2:188411000-188418800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:188411200-188419000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:188412000-188415600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:188412400-188415600	Weak transcription	Pancreas	Pancrea
19	chr2:188412600-188415600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:188412600-188415600	Weak transcription	Dnd41	blood
21	chr2:188412600-188416000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr2:188412600-188417600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:188412600-188418200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:188412600-188418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:188412800-188415600	Weak transcription	NH-A	brain
26	chr2:188413200-188415600	Active TSS	Psoas Muscle	Psoas
27	chr2:188413200-188417200	Weak transcription	Fetal Stomach	stomach
28	chr2:188413200-188417400	Enhancers	Stomach Mucosa	stomach
29	chr2:188413400-188417800	Weak transcription	HMEC	breast
30	chr2:188413400-188417800	Weak transcription	NHEK	skin
31	chr2:188413400-188418800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:188413600-188419800	Active TSS	Right Atrium	heart
33	chr2:188413800-188417800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:188414000-188416600	Flanking Active TSS	HUVEC	blood vessel
35	chr2:188414000-188416800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:188414000-188417200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:188414200-188415600	Active TSS	NHLF	lung
38	chr2:188414200-188416000	Enhancers	Hela-S3	cervix
39	chr2:188414200-188417400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr2:188414400-188416600	Flanking Active TSS	HepG2	liver
41	chr2:188414600-188416400	Active TSS	Right Ventricle	heart
42	chr2:188414600-188416400	Active TSS	Stomach Smooth Muscle	stomach
43	chr2:188414600-188416600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:188414600-188417800	Enhancers	Fetal Intestine Small	intestine
45	chr2:188414600-188419600	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr2:188414800-188415600	Active TSS	HSMMtube	muscle
47	chr2:188414800-188416200	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr2:188414800-188416400	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr2:188414800-188416400	Flanking Active TSS	A549	lung
50	chr2:188414800-188416400	Transcr. at gene 5' and 3'	HSMM	muscle

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