Variant report

Variant	rs4953588
Chromosome Location	chr2:48738042-48738043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48731834..48734173-chr2:48736492..48738374,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10185212	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap]
rs11125172	1.00[EUR][1000 genomes]
rs11677398	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11695461	1.00[EUR][1000 genomes]
rs12477901	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs13386132	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs3811520	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4328683	1.00[CEU][hapmap]
rs4371401	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4429520	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4430989	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4464333	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4564825	1.00[EUR][1000 genomes]
rs4952913	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4953584	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap]
rs6545040	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6545042	1.00[EUR][1000 genomes]
rs6545043	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6545044	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6715766	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6744619	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6756820	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7355307	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7608588	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][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	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
2	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48694200-48753000	Weak transcription	Psoas Muscle	Psoas
2	chr2:48707400-48742000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:48709400-48755200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:48710200-48745000	Weak transcription	Fetal Brain Male	brain
5	chr2:48722600-48741800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:48723800-48748200	Strong transcription	GM12878-XiMat	blood
7	chr2:48724400-48738400	Weak transcription	Fetal Heart	heart
8	chr2:48726200-48742400	Weak transcription	Colonic Mucosa	Colon
9	chr2:48726400-48756800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:48728200-48756800	Weak transcription	HMEC	breast
11	chr2:48728600-48738400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:48728800-48741800	Weak transcription	Spleen	Spleen
13	chr2:48729000-48742800	Weak transcription	Right Ventricle	heart
14	chr2:48729600-48742800	Weak transcription	Esophagus	oesophagus
15	chr2:48729800-48738200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:48732200-48751400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:48732400-48740000	Strong transcription	Fetal Muscle Leg	muscle
18	chr2:48732400-48743400	Strong transcription	Primary hematopoietic stem cells	blood
19	chr2:48732400-48749600	Strong transcription	Primary B cells from cord blood	blood
20	chr2:48732800-48740000	Strong transcription	Fetal Muscle Trunk	muscle
21	chr2:48733400-48742400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:48734200-48739800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr2:48735200-48738200	Enhancers	Hela-S3	cervix
24	chr2:48735200-48738400	Weak transcription	Lung	lung
25	chr2:48735200-48739600	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:48735400-48740200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:48735400-48740400	Strong transcription	Brain Germinal Matrix	brain
28	chr2:48735600-48740200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:48735800-48738400	Weak transcription	Fetal Stomach	stomach
30	chr2:48736000-48738200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:48736000-48738200	Enhancers	Osteobl	bone
32	chr2:48736000-48738400	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:48736000-48738400	Weak transcription	HSMMtube	muscle
34	chr2:48736000-48739200	Weak transcription	Brain Angular Gyrus	brain
35	chr2:48736000-48741800	Weak transcription	Fetal Brain Female	brain
36	chr2:48736000-48742800	Weak transcription	Aorta	Aorta
37	chr2:48736000-48742800	Weak transcription	Gastric	stomach
38	chr2:48736000-48742800	Weak transcription	Ovary	ovary
39	chr2:48736000-48742800	Weak transcription	Pancreas	Pancrea
40	chr2:48736000-48752800	Weak transcription	Small Intestine	intestine
41	chr2:48736200-48739400	Weak transcription	A549	lung
42	chr2:48736200-48740000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr2:48736200-48749400	Strong transcription	Primary B cells from peripheral blood	blood
44	chr2:48736200-48749400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:48736400-48738400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:48736400-48738400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:48736400-48739000	Weak transcription	NHLF	lung
48	chr2:48736400-48739200	Weak transcription	Fetal Lung	lung
49	chr2:48736400-48739400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:48736400-48740000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood

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