Variant report

Variant	rs4972352
Chromosome Location	chr2:149056416-149056417
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10153599	0.89[AMR][1000 genomes]
rs10168750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10168759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10177233	1.00[AMR][1000 genomes]
rs10188956	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10208949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10928387	1.00[AMR][1000 genomes]
rs10928392	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11692197	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12472437	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12691783	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1377455	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1453316	0.89[AFR][1000 genomes]
rs1470862	0.96[YRI][hapmap];1.00[AMR][1000 genomes]
rs1542323	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1869342	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1992989	1.00[AMR][1000 genomes]
rs2034672	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2123617	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2167881	0.81[AMR][1000 genomes]
rs2167882	1.00[AMR][1000 genomes]
rs2219066	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2656318	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2890919	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs4972339	1.00[AMR][1000 genomes]
rs4972340	1.00[AMR][1000 genomes]
rs4972344	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4972350	0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4972351	0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4972353	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55721902	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57396192	1.00[EUR][1000 genomes]
rs6430307	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6709521	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6722460	1.00[AMR][1000 genomes]
rs6725093	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6726373	1.00[AMR][1000 genomes]
rs73015168	1.00[EUR][1000 genomes]
rs73015181	1.00[EUR][1000 genomes]
rs73019226	1.00[EUR][1000 genomes]
rs7424220	1.00[AMR][1000 genomes]
rs7569947	1.00[AMR][1000 genomes]
rs7572485	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7573171	1.00[AMR][1000 genomes]
rs7586070	1.00[EUR][1000 genomes]
rs7586436	1.00[EUR][1000 genomes]
rs7588000	0.89[AMR][1000 genomes]
rs7602337	1.00[AFR][1000 genomes];1.00[AMR][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:42 , 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	chr2:149045600-149060600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:149045600-149070600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:149050600-149062600	Weak transcription	Fetal Stomach	stomach
15	chr2:149052800-149058400	Weak transcription	Aorta	Aorta
16	chr2:149053000-149060600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:149053800-149057800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:149054600-149057800	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:149054800-149057800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:149055200-149072400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr2:149055400-149056600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:149055400-149058600	Weak transcription	Brain Germinal Matrix	brain
23	chr2:149055600-149056600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:149055600-149060200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:149055800-149059200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr2:149055800-149059400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:149055800-149059600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:149055800-149059600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:149056000-149058000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:149056000-149058200	Weak transcription	Osteobl	bone
31	chr2:149056000-149059000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:149056000-149059200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:149056000-149059600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:149056000-149060200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:149056000-149060800	Weak transcription	NH-A	brain
36	chr2:149056000-149061600	Weak transcription	Primary B cells from cord blood	blood
37	chr2:149056000-149063000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr2:149056000-149070000	Weak transcription	Primary T cells from cord blood	blood
39	chr2:149056000-149076400	Weak transcription	Esophagus	oesophagus
40	chr2:149056200-149057400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:149056400-149056800	Strong transcription	Thymus	Thymus
42	chr2:149056400-149058000	Weak transcription	Muscle Satellite Cultured Cells	--

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