Variant report

Variant	rs4894048
Chromosome Location	chr2:179638721-179638722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10171049	0.81[GIH][hapmap]
rs10176708	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10179219	0.83[AMR][1000 genomes]
rs10179811	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10183237	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10183361	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10203085	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10221590	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10497519	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10497522	1.00[CEU][hapmap];0.88[GIH][hapmap]
rs11888217	0.81[GIH][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11895382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11897386	1.00[CEU][hapmap]
rs13386186	1.00[ASN][1000 genomes]
rs13392492	0.83[AMR][1000 genomes]
rs13398235	0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13421990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1484120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1565288	0.80[AMR][1000 genomes]
rs16866473	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16866519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17355623	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1905520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2291310	0.81[GIH][hapmap]
rs2291311	0.81[GIH][hapmap]
rs2291312	0.81[GIH][hapmap]
rs2366752	1.00[CEU][hapmap]
rs3754953	0.81[GIH][hapmap]
rs4893852	0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4893853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4894040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4894041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4894045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4894052	1.00[CHB][hapmap]
rs72647887	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72647888	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7572955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7585334	0.81[GIH][hapmap]
rs7604033	0.81[GIH][hapmap]

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	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv962089	chr2:179635536-179643793	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179483200-179655400	Weak transcription	Adipose Nuclei	Adipose
2	chr2:179533600-179669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:179577800-179640800	Weak transcription	Fetal Intestine Large	intestine
4	chr2:179590800-179640400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr2:179605400-179662400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:179610800-179671400	Weak transcription	Ovary	ovary
7	chr2:179614200-179645200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:179622600-179640600	Weak transcription	Pancreas	Pancrea
9	chr2:179627000-179655200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:179627400-179653200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:179627600-179639200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr2:179627600-179652600	Weak transcription	Brain Substantia Nigra	brain
13	chr2:179627600-179663800	Weak transcription	Thymus	Thymus
14	chr2:179629600-179666200	Weak transcription	GM12878-XiMat	blood
15	chr2:179630600-179651000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr2:179630800-179640800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:179631200-179649800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:179632000-179658800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:179632400-179667800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:179632800-179641000	Weak transcription	Fetal Thymus	thymus
21	chr2:179634200-179648600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:179634400-179645200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:179635200-179640800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:179635600-179640800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:179635600-179640800	Weak transcription	Fetal Muscle Trunk	muscle
26	chr2:179635800-179640800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:179636200-179641000	Weak transcription	Right Ventricle	heart
28	chr2:179636200-179643000	Weak transcription	HSMM	muscle
29	chr2:179636200-179647000	Weak transcription	Lung	lung
30	chr2:179636200-179660600	Weak transcription	Brain Anterior Caudate	brain
31	chr2:179637200-179639600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
32	chr2:179637200-179651000	Strong transcription	Primary T cells from cord blood	blood
33	chr2:179637200-179651000	Strong transcription	HSMMtube	muscle
34	chr2:179637400-179641400	Genic enhancers	Fetal Heart	heart
35	chr2:179637400-179643800	Strong transcription	Primary B cells from cord blood	blood
36	chr2:179637600-179640200	Strong transcription	Left Ventricle	heart
37	chr2:179637600-179641200	Strong transcription	Psoas Muscle	Psoas
38	chr2:179637600-179647000	Strong transcription	Fetal Muscle Leg	muscle
39	chr2:179638400-179639400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:179638600-179638800	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
41	chr2:179638600-179639200	Strong transcription	Primary B cells from peripheral blood	blood

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