Variant report

Variant	rs12477901
Chromosome Location	chr2:48711523-48711524
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10164898	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10185212	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11125172	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11677398	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11695461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13386132	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];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4429520	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4430989	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4464333	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4564825	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4952913	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4953582	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4953584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4953585	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4953588	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6545040	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6545042	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545043	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545044	1.00[CEU][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6715766	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6744619	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[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]
rs7557764	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7608588	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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	chr2:48673200-48724000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:48682600-48716200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:48689200-48735600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:48690000-48735600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:48694000-48729400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:48694200-48753000	Weak transcription	Psoas Muscle	Psoas
7	chr2:48695200-48723800	Weak transcription	Gastric	stomach
8	chr2:48695200-48725800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:48695200-48728000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:48695400-48728000	Weak transcription	Hela-S3	cervix
11	chr2:48695600-48713400	Weak transcription	Colonic Mucosa	Colon
12	chr2:48695600-48735200	Weak transcription	K562	blood
13	chr2:48696200-48721000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:48696400-48716400	Weak transcription	Right Ventricle	heart
15	chr2:48696400-48721600	Weak transcription	Left Ventricle	heart
16	chr2:48696400-48723800	Weak transcription	Aorta	Aorta
17	chr2:48698600-48723200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:48698800-48729200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:48698800-48735400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr2:48700200-48735400	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:48700600-48718400	Strong transcription	Primary T cells from cord blood	blood
22	chr2:48700600-48735600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr2:48701600-48714400	Strong transcription	GM12878-XiMat	blood
24	chr2:48701800-48715000	Weak transcription	NHDF-Ad	bronchial
25	chr2:48702000-48716400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:48703200-48723400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:48703200-48729800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:48704000-48712400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:48704000-48718600	Strong transcription	Fetal Thymus	thymus
30	chr2:48704000-48735800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:48704200-48716800	Strong transcription	Placenta	Placenta
32	chr2:48704400-48718600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:48704400-48730000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr2:48704600-48717000	Strong transcription	Primary B cells from cord blood	blood
35	chr2:48704600-48735400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:48704600-48735600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr2:48704800-48711600	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:48705400-48713600	Weak transcription	HSMM	muscle
39	chr2:48705400-48716200	Weak transcription	Esophagus	oesophagus
40	chr2:48705600-48712000	Enhancers	Rectal Smooth Muscle	rectum
41	chr2:48705800-48713200	Weak transcription	HSMMtube	muscle
42	chr2:48705800-48715000	Weak transcription	A549	lung
43	chr2:48706600-48716600	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:48706600-48728000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:48707000-48715800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:48707400-48712000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:48707400-48713800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:48707400-48742000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:48707600-48711600	Enhancers	Colon Smooth Muscle	Colon
50	chr2:48707600-48712000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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