Variant report

Variant	rs11677398
Chromosome Location	chr2:48741595-48741596
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10164898	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10185212	1.00[CEU][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11125172	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11695461	0.88[AMR][1000 genomes]
rs12477901	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13386132	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3811520	1.00[CEU][hapmap]
rs4328683	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4371401	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4429520	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4430989	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4464333	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4564825	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4952913	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4953574	1.00[EUR][1000 genomes]
rs4953582	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4953584	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs4953585	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4953586	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4953588	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4953590	0.87[EUR][1000 genomes]
rs6545040	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6545042	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6545043	1.00[CEU][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6545044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6715766	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes]
rs6744619	0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6756820	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7355307	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7557764	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7577850	1.00[EUR][1000 genomes]
rs7608588	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][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	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
2	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
3	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:122 , 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	chr2:48726200-48742400	Weak transcription	Colonic Mucosa	Colon
8	chr2:48726400-48756800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:48728200-48756800	Weak transcription	HMEC	breast
10	chr2:48728800-48741800	Weak transcription	Spleen	Spleen
11	chr2:48729000-48742800	Weak transcription	Right Ventricle	heart
12	chr2:48729600-48742800	Weak transcription	Esophagus	oesophagus
13	chr2:48732200-48751400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:48732400-48743400	Strong transcription	Primary hematopoietic stem cells	blood
15	chr2:48732400-48749600	Strong transcription	Primary B cells from cord blood	blood
16	chr2:48733400-48742400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:48736000-48741800	Weak transcription	Fetal Brain Female	brain
18	chr2:48736000-48742800	Weak transcription	Aorta	Aorta
19	chr2:48736000-48742800	Weak transcription	Gastric	stomach
20	chr2:48736000-48742800	Weak transcription	Ovary	ovary
21	chr2:48736000-48742800	Weak transcription	Pancreas	Pancrea
22	chr2:48736000-48752800	Weak transcription	Small Intestine	intestine
23	chr2:48736200-48749400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr2:48736200-48749400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:48736400-48742600	Weak transcription	Stomach Mucosa	stomach
26	chr2:48736400-48748400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:48736400-48749600	Strong transcription	Liver	Liver
28	chr2:48736400-48750000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:48736400-48752600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:48736400-48753400	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr2:48736400-48754600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:48736600-48746600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:48736600-48749600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:48736600-48749800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr2:48736800-48747200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:48736800-48749400	Strong transcription	Fetal Thymus	thymus
37	chr2:48736800-48749600	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr2:48737000-48744400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:48737000-48748200	Strong transcription	Duodenum Mucosa	Duodenum
40	chr2:48737000-48748600	Strong transcription	Dnd41	blood
41	chr2:48737000-48749600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:48737000-48749600	Strong transcription	Brain Anterior Caudate	brain
43	chr2:48737200-48750600	Strong transcription	Fetal Intestine Large	intestine
44	chr2:48737400-48747000	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr2:48737600-48744800	Strong transcription	HepG2	liver
46	chr2:48737600-48747000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:48737600-48749800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:48737600-48750200	Strong transcription	Primary T cells from cord blood	blood
49	chr2:48737800-48741800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:48737800-48749400	Strong transcription	Primary T helper cells fromperipheralblood	blood

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