Variant report

Variant	rs11678688
Chromosome Location	chr2:149055476-149055477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10196090	0.86[EUR][1000 genomes]
rs10208839	0.84[EUR][1000 genomes]
rs10432369	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11675979	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676308	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11683219	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11692246	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12053104	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12470061	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478120	0.82[EUR][1000 genomes]
rs12618358	0.93[EUR][1000 genomes]
rs13001946	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13022005	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13032996	0.88[AMR][1000 genomes]
rs1453317	0.95[EUR][1000 genomes]
rs1453318	0.84[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1580063	0.93[ASN][1000 genomes]
rs17274896	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17276501	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1869341	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084954	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2167880	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2602352	0.94[EUR][1000 genomes]
rs2602358	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2656317	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2656319	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656320	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656324	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656325	0.95[EUR][1000 genomes]
rs2839755	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28831467	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2938705	0.95[EUR][1000 genomes]
rs35042809	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4972277	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4972278	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972347	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972355	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972358	0.94[EUR][1000 genomes]
rs6734448	0.94[EUR][1000 genomes]
rs6746932	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7572948	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7592019	0.86[EUR][1000 genomes]
rs869595	0.94[EUR][1000 genomes]
rs949679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs987625	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs987626	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869146	chr2:148787051-149060763	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv2753542	chr2:149004714-149268503	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1012275	chr2:149031668-149316793	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv523090	chr2:149037012-149110873	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:149012800-149096000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:149017400-149062800	Weak transcription	Fetal Lung	lung
3	chr2:149017400-149070600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr2:149017600-149060800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:149026000-149070400	Weak transcription	Fetal Intestine Small	intestine
6	chr2:149031400-149079000	Weak transcription	Left Ventricle	heart
7	chr2:149041600-149058200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:149042200-149070600	Weak transcription	Ovary	ovary
9	chr2:149042600-149057600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr2:149042800-149058000	Weak transcription	HSMM	muscle
11	chr2:149043400-149063600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:149045600-149055600	Weak transcription	Primary B cells from cord blood	blood
13	chr2:149045600-149060600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:149045600-149070600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:149050600-149062600	Weak transcription	Fetal Stomach	stomach
16	chr2:149050800-149056400	Weak transcription	Thymus	Thymus
17	chr2:149052800-149058400	Weak transcription	Aorta	Aorta
18	chr2:149053000-149060600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:149053800-149057800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:149054600-149057800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr2:149054800-149055600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:149054800-149057800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:149055200-149055800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr2:149055200-149056000	Strong transcription	Primary T cells from cord blood	blood
25	chr2:149055200-149072400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:149055400-149055800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr2:149055400-149055800	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr2:149055400-149055800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr2:149055400-149056000	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr2:149055400-149056000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr2:149055400-149056600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:149055400-149058600	Weak transcription	Brain Germinal Matrix	brain

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