Variant report

Variant	rs4953419
Chromosome Location	chr2:46989869-46989870
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46988369..46990736-chr2:46993242..46995389,2	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1058157	0.83[CEU][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1109380	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11676737	0.83[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11695058	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12474201	0.83[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap]
rs12998753	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12998762	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12999586	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13025595	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13025984	0.83[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13031872	0.83[AMR][1000 genomes]
rs13429704	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17822019	0.87[ASW][hapmap];0.83[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17822294	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2346878	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34401107	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35158352	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35722922	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35825831	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3829835	0.83[CEU][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4952842	0.83[CEU][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[AMR][1000 genomes]
rs4952843	0.87[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6738426	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7562173	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7584870	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7594523	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs897530	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[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	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv1013079	chr2:46949337-46998417	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46974600-46990000	Weak transcription	Colonic Mucosa	Colon
2	chr2:46976200-46990400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:46981200-46991000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:46981400-47006800	Weak transcription	Psoas Muscle	Psoas
5	chr2:46981800-46993200	Weak transcription	Fetal Heart	heart
6	chr2:46983200-46990400	Strong transcription	Osteobl	bone
7	chr2:46984400-46998600	Weak transcription	Fetal Brain Male	brain
8	chr2:46985000-46990200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:46985200-46991400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:46985600-46998600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:46985600-47008200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:46987000-46993000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:46987200-46990200	Weak transcription	Placenta	Placenta
14	chr2:46987200-46995000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:46987200-46996200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:46987200-46997800	Weak transcription	Liver	Liver
17	chr2:46987400-46990400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:46987400-46990400	Weak transcription	Esophagus	oesophagus
19	chr2:46987400-46990400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:46987400-46991000	Weak transcription	Ovary	ovary
21	chr2:46987400-46991000	Weak transcription	A549	lung
22	chr2:46987400-46991200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr2:46987400-46991400	Weak transcription	NHLF	lung
24	chr2:46987400-46991600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr2:46987400-46992800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:46987400-46992800	Weak transcription	HSMMtube	muscle
27	chr2:46987400-46993200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:46987400-46993400	Weak transcription	Pancreas	Pancrea
29	chr2:46987400-46997000	Weak transcription	Fetal Lung	lung
30	chr2:46987400-46997400	Weak transcription	Fetal Stomach	stomach
31	chr2:46987400-46997600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:46987400-46997600	Weak transcription	Fetal Intestine Small	intestine
33	chr2:46987400-47005600	Weak transcription	Fetal Muscle Leg	muscle
34	chr2:46987400-47005600	Weak transcription	Left Ventricle	heart
35	chr2:46987600-46990200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:46987600-46990200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:46987600-46990200	Weak transcription	Fetal Kidney	kidney
38	chr2:46987600-46990800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:46987600-46991000	Weak transcription	Primary B cells from cord blood	blood
40	chr2:46987600-46991400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:46987600-46993800	Weak transcription	Primary T cells from cord blood	blood
42	chr2:46987600-46995000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:46987600-46997000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:46987600-46997200	Weak transcription	HSMM	muscle
45	chr2:46987600-46997400	Weak transcription	Fetal Intestine Large	intestine
46	chr2:46987600-47006000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:46987800-46997200	Weak transcription	NH-A	brain
48	chr2:46988200-46990000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:46988200-46991000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr2:46988200-46991000	Weak transcription	HepG2	liver

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