Variant report

Variant	rs13427829
Chromosome Location	chr2:188404283-188404284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:188365827..188368256-chr2:188403673..188406049,2	MCF-7	breast:
2	chr2:188382405..188385031-chr2:188403850..188405817,2	K562	blood:
3	chr2:188389696..188391580-chr2:188402374..188405162,2	K562	blood:
4	chr2:188367231..188371096-chr2:188401019..188405423,6	K562	blood:
5	chr2:188398970..188401688-chr2:188404214..188406089,3	K562	blood:

Variant related genes	Relation type
ENSG00000003436	Chromatin interaction

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

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

rs_ID	r²[population]
rs10153820	0.84[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10177003	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10185334	0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10191373	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11902917	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13411086	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]
rs13425112	0.91[ASN][1000 genomes]
rs4366866	0.88[ASN][1000 genomes]
rs4643503	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4666732	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4666734	0.89[ASN][1000 genomes]
rs4667168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56141195	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56170850	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60452662	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6434222	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6434223	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6715871	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6749781	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6756052	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73052654	0.87[ASN][1000 genomes]
rs73052656	0.86[ASN][1000 genomes]
rs73982974	0.87[ASN][1000 genomes]
rs9288142	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	nsv875564	chr2:188258904-188414161	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	nsv834488	chr2:188268434-188415496	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188381800-188406000	Weak transcription	Small Intestine	intestine
2	chr2:188381800-188406600	Weak transcription	Aorta	Aorta
3	chr2:188385200-188406000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:188387000-188406000	Weak transcription	Fetal Intestine Large	intestine
5	chr2:188387200-188406000	Weak transcription	HSMMtube	muscle
6	chr2:188391800-188405800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:188392200-188413200	Weak transcription	Psoas Muscle	Psoas
8	chr2:188392400-188409200	Weak transcription	Ovary	ovary
9	chr2:188393000-188404800	Weak transcription	NH-A	brain
10	chr2:188393000-188406200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:188394800-188405800	Weak transcription	NHLF	lung
12	chr2:188394800-188408400	Weak transcription	K562	blood
13	chr2:188395400-188405800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:188396000-188404800	Weak transcription	Osteobl	bone
15	chr2:188397800-188405800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:188397800-188406400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:188398000-188409200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:188398200-188404800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:188398200-188404800	Weak transcription	Fetal Stomach	stomach
20	chr2:188398200-188406000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:188398200-188406000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:188398200-188406000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:188398200-188406000	Weak transcription	Fetal Intestine Small	intestine
24	chr2:188398200-188409200	Weak transcription	Lung	lung
25	chr2:188398200-188409200	Weak transcription	Pancreas	Pancrea
26	chr2:188398200-188409600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:188398200-188409600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:188398400-188404600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:188398400-188406600	Weak transcription	Placenta	Placenta
30	chr2:188398400-188418000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:188400000-188405800	Weak transcription	Liver	Liver
32	chr2:188401800-188408000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr2:188402200-188406000	Weak transcription	Fetal Lung	lung
34	chr2:188403200-188404600	Strong transcription	HSMM	muscle
35	chr2:188403200-188404800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:188403200-188405800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:188403400-188406000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:188403400-188406000	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:188403600-188405000	Strong transcription	HUVEC	blood vessel
40	chr2:188403600-188406000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:188403600-188406200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:188403800-188404400	Genic enhancers	Hela-S3	cervix
43	chr2:188403800-188405400	Genic enhancers	Muscle Satellite Cultured Cells	--
44	chr2:188403800-188405800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:188403800-188407000	Enhancers	HepG2	liver
46	chr2:188404000-188404600	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr2:188404000-188405200	Flanking Active TSS	A549	lung
48	chr2:188404200-188404400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:188404200-188405200	Enhancers	NHDF-Ad	bronchial
50	chr2:188404200-188405800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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