Variant report

Variant	rs1962588
Chromosome Location	chr2:30465122-30465123
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	chr2:30463829..30466143-chr2:30472791..30475972,4	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1001204	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10171296	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs10171305	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs11676884	0.92[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs13386455	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13389106	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17009304	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17009315	0.81[CEU][hapmap]
rs17321999	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2089657	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2362541	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs3813658	0.92[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs3817143	0.89[EUR][1000 genomes]
rs4384829	0.92[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs4564821	0.92[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs4952115	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58645306	0.90[ASN][1000 genomes]
rs59693338	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6548005	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6708792	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6732241	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72787716	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72787718	0.90[ASN][1000 genomes]
rs72787719	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72787721	0.89[EUR][1000 genomes]
rs72787722	0.90[EUR][1000 genomes]
rs72787724	0.89[EUR][1000 genomes]
rs73925103	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7604484	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs906865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs906866	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs906867	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9309678	0.90[EUR][1000 genomes]
rs9558	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs9798481	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer 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	32 gene(s)	inside rSNPs	diseases
2	nsv1002657	chr2:30339312-30516535	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv2662	chr2:30462905-30495134	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30457000-30476600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:30457200-30470400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:30457200-30473000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:30457400-30466400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:30457600-30471800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:30457800-30467400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:30457800-30481000	Weak transcription	Gastric	stomach
8	chr2:30458400-30475800	Weak transcription	Fetal Kidney	kidney
9	chr2:30460800-30471800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:30461000-30479800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:30461400-30469400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
12	chr2:30461800-30465400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:30461800-30472200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:30462200-30473200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:30462400-30468200	Weak transcription	GM12878-XiMat	blood
16	chr2:30462600-30468200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:30462600-30468200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:30462800-30466600	Strong transcription	NH-A	brain
19	chr2:30462800-30471200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:30462800-30474800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:30462800-30475400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr2:30463000-30467400	Genic enhancers	A549	lung
23	chr2:30463000-30471000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:30463000-30473000	Weak transcription	Fetal Intestine Small	intestine
25	chr2:30463000-30474200	Weak transcription	Fetal Intestine Large	intestine
26	chr2:30463000-30474800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:30463000-30475400	Genic enhancers	Primary T cells fromperipheralblood	blood
28	chr2:30463200-30466200	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:30463200-30466800	Weak transcription	Fetal Brain Female	brain
30	chr2:30463200-30471200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:30463400-30465800	Weak transcription	Fetal Brain Male	brain
32	chr2:30463400-30466200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:30463400-30467000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr2:30463400-30472400	Strong transcription	HSMM	muscle
35	chr2:30463400-30473400	Weak transcription	Ovary	ovary
36	chr2:30463400-30474800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:30463400-30474800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:30463400-30475000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr2:30463400-30475400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr2:30463400-30475600	Weak transcription	Brain Germinal Matrix	brain
41	chr2:30463400-30475600	Weak transcription	Colon Smooth Muscle	Colon
42	chr2:30463400-30475600	Weak transcription	Esophagus	oesophagus
43	chr2:30463600-30466000	Weak transcription	Aorta	Aorta
44	chr2:30463600-30466400	Weak transcription	Fetal Stomach	stomach
45	chr2:30463600-30468400	Weak transcription	Spleen	Spleen
46	chr2:30463600-30472200	Weak transcription	Lung	lung
47	chr2:30463600-30472200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:30463600-30472400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:30463600-30473200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:30463600-30475600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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