Variant report

Variant	rs4372840
Chromosome Location	chr2:184031083-184031084
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10497620	0.80[ASN][1000 genomes]
rs11682917	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1462534	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16823723	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16824018	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16824025	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16824033	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16824048	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16824058	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16824059	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16824095	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16824106	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17706149	0.84[ASN][1000 genomes]
rs1997486	0.80[ASN][1000 genomes]
rs2017742	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2176232	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2368372	0.95[EUR][1000 genomes]
rs2368373	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35453132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748881	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3748882	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3762476	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4606882	1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4666611	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4666612	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4666620	0.84[ASN][1000 genomes]
rs4666890	0.84[ASN][1000 genomes]
rs4666892	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4666896	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4666898	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56402172	0.80[ASN][1000 genomes]
rs72892678	0.80[ASN][1000 genomes]
rs72892681	0.80[ASN][1000 genomes]
rs72892682	0.80[ASN][1000 genomes]
rs72892683	0.80[ASN][1000 genomes]
rs72892686	0.92[ASN][1000 genomes]
rs72892687	0.92[ASN][1000 genomes]
rs72892688	0.80[ASN][1000 genomes]
rs72892690	0.80[ASN][1000 genomes]
rs72894514	0.80[ASN][1000 genomes]
rs72894558	0.81[ASN][1000 genomes]
rs72896596	0.84[ASN][1000 genomes]
rs72896599	0.84[ASN][1000 genomes]
rs7591252	0.84[ASN][1000 genomes]
rs9333281	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9333283	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1010799	chr2:183855680-184244721	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS 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	20 gene(s)	inside rSNPs	diseases
5	nsv536072	chr2:183855680-184244721	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	esv2763287	chr2:183939173-184037893	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers 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
7	nsv875486	chr2:184016627-184095979	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv821842	chr2:184030701-184037931	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183990000-184050000	Weak transcription	Aorta	Aorta
2	chr2:183990200-184036400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:183991000-184048400	Weak transcription	Brain Angular Gyrus	brain
4	chr2:183991000-184053400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:183991000-184055400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:183991200-184035400	Weak transcription	Fetal Brain Male	brain
7	chr2:183991400-184034000	Weak transcription	NHLF	lung
8	chr2:183991400-184049600	Weak transcription	NHDF-Ad	bronchial
9	chr2:183992400-184047600	Weak transcription	Hela-S3	cervix
10	chr2:184009000-184043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:184009200-184034000	Weak transcription	Esophagus	oesophagus
12	chr2:184009200-184043600	Weak transcription	Psoas Muscle	Psoas
13	chr2:184009200-184048400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:184009400-184047200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:184014200-184031400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:184015000-184062000	Weak transcription	Small Intestine	intestine
17	chr2:184018400-184047400	Weak transcription	Pancreas	Pancrea
18	chr2:184019000-184031200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:184019000-184036600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:184019000-184043600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:184019000-184050000	Weak transcription	Gastric	stomach
22	chr2:184019000-184053400	Weak transcription	Placenta	Placenta
23	chr2:184022000-184031200	Strong transcription	Dnd41	blood
24	chr2:184023000-184031400	Strong transcription	Fetal Thymus	thymus
25	chr2:184023000-184033000	Strong transcription	Primary T cells from cord blood	blood
26	chr2:184023400-184034200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:184024200-184031200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr2:184024200-184031400	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr2:184025000-184031200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:184025000-184031400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:184025000-184031400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:184025200-184031200	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:184025200-184031200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:184025200-184031400	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr2:184025600-184031800	Strong transcription	A549	lung
36	chr2:184026000-184054600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:184026000-184057600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:184026600-184043200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:184026600-184058800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr2:184026800-184047400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:184027400-184035800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:184027600-184057600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr2:184028600-184045600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:184028800-184043200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:184028800-184043600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:184029000-184036400	Weak transcription	Spleen	Spleen
47	chr2:184029000-184047400	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr2:184029200-184036800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr2:184029200-184043000	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:184029200-184043200	Weak transcription	H9 Cell Line	embryonic stem cell

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