Variant report

Variant	rs949679
Chromosome Location	chr2:149061500-149061501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
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]
rs11678688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	0.86[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]
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:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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:43 , 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	chr2:149026000-149070400	Weak transcription	Fetal Intestine Small	intestine
5	chr2:149031400-149079000	Weak transcription	Left Ventricle	heart
6	chr2:149042200-149070600	Weak transcription	Ovary	ovary
7	chr2:149043400-149063600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:149045600-149070600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:149050600-149062600	Weak transcription	Fetal Stomach	stomach
10	chr2:149055200-149072400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr2:149056000-149061600	Weak transcription	Primary B cells from cord blood	blood
12	chr2:149056000-149063000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:149056000-149070000	Weak transcription	Primary T cells from cord blood	blood
14	chr2:149056000-149076400	Weak transcription	Esophagus	oesophagus
15	chr2:149056600-149070800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:149056800-149070600	Weak transcription	Thymus	Thymus
17	chr2:149057800-149064000	Enhancers	Fetal Brain Male	brain
18	chr2:149058600-149062400	Enhancers	Brain Germinal Matrix	brain
19	chr2:149058600-149063000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:149058600-149063000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:149058600-149076400	Weak transcription	Aorta	Aorta
22	chr2:149059200-149064800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr2:149059400-149063000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:149059400-149100400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr2:149059600-149063400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:149059600-149064000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr2:149059600-149064600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr2:149060000-149063000	Weak transcription	HSMMtube	muscle
29	chr2:149060200-149062000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr2:149060200-149062200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:149060200-149064000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:149060400-149063000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:149060600-149061600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:149060600-149063800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr2:149060800-149062000	Enhancers	Fetal Brain Female	brain
36	chr2:149061000-149070400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:149061200-149061600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:149061200-149061800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr2:149061200-149062200	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr2:149061200-149062400	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr2:149061200-149063200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:149061200-149095800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr2:149061400-149065200	Enhancers	HUES48 Cell Line	embryonic stem cell

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