Variant report

Variant	rs4952354
Chromosome Location	chr2:40343047-40343048
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10183046	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs10490206	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11676744	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11680622	0.82[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes]
rs11687766	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12464756	0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12466767	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12470980	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12478057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12712683	0.82[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13005439	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs17501526	0.81[CEU][hapmap];0.87[AMR][1000 genomes]
rs17559580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17559651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2005886	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2072532	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2110926	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2373791	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2373792	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2888657	0.85[CEU][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes]
rs5542	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5551	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56090875	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60563966	0.98[ASN][1000 genomes]
rs62150869	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62150874	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6742885	0.85[JPT][hapmap]
rs929642	0.85[CEU][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833892	chr2:40188785-40363480	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv873903	chr2:40285145-40382712	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv873905	chr2:40341847-40364895	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv873906	chr2:40341847-40385045	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40321200-40354600	Weak transcription	Right Ventricle	heart
2	chr2:40322800-40350200	Weak transcription	Fetal Brain Male	brain
3	chr2:40328000-40365600	Weak transcription	Brain Germinal Matrix	brain
4	chr2:40329800-40345200	Weak transcription	Fetal Thymus	thymus
5	chr2:40331200-40350200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:40331200-40351200	Weak transcription	Fetal Stomach	stomach
7	chr2:40333000-40351000	Weak transcription	Aorta	Aorta
8	chr2:40333400-40354400	Weak transcription	NH-A	brain
9	chr2:40334600-40354800	Weak transcription	Fetal Brain Female	brain
10	chr2:40336600-40345600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:40339000-40345800	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:40340200-40345200	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr2:40340200-40345600	Weak transcription	Small Intestine	intestine
14	chr2:40340600-40351000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:40340800-40343400	Weak transcription	Spleen	Spleen
16	chr2:40340800-40343400	Strong transcription	Dnd41	blood
17	chr2:40340800-40350000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:40341000-40344400	Genic enhancers	Fetal Heart	heart
19	chr2:40341200-40343200	Weak transcription	Ovary	ovary
20	chr2:40341200-40345600	Weak transcription	Lung	lung
21	chr2:40341400-40343200	Genic enhancers	Left Ventricle	heart
22	chr2:40341600-40343200	Strong transcription	HSMM	muscle
23	chr2:40341600-40345000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:40341600-40350200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:40341600-40357000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:40341800-40350800	Weak transcription	Right Atrium	heart
27	chr2:40342400-40349800	Weak transcription	Osteobl	bone
28	chr2:40342600-40343200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:40342600-40343200	Enhancers	HMEC	breast
30	chr2:40342800-40343200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:40342800-40345000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:40342800-40357600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:40343000-40343400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:40343000-40349600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:40343000-40350200	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:40343000-40351000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:40343000-40354800	Weak transcription	Stomach Smooth Muscle	stomach

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