Variant report

Variant	rs13388291
Chromosome Location	chr2:48545582-48545583
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10153773	1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs10174717	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10180295	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10186237	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10193072	0.95[ASN][1000 genomes]
rs10199431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10208124	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10454133	0.82[CEU][hapmap]
rs10495951	0.86[JPT][hapmap]
rs10495952	0.86[JPT][hapmap]
rs11676168	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11679523	0.86[JPT][hapmap]
rs11680916	0.90[JPT][hapmap]
rs11682044	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11685861	0.92[CEU][hapmap];0.86[JPT][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs11688481	0.86[JPT][hapmap]
rs11690690	0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11690748	0.86[JPT][hapmap]
rs11690845	0.86[JPT][hapmap]
rs12616792	0.86[ASN][1000 genomes]
rs12713008	0.86[ASN][1000 genomes]
rs12713009	0.85[ASN][1000 genomes]
rs13383364	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13385535	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13386751	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13387171	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13426834	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13432998	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17037289	0.86[JPT][hapmap]
rs17037298	0.86[JPT][hapmap]
rs17855177	0.86[JPT][hapmap]
rs2471405	0.84[ASN][1000 genomes]
rs28806843	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28841370	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4290706	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4344965	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs4411759	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4547573	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4641990	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs56352447	0.95[ASN][1000 genomes]
rs57668696	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58660534	0.88[ASN][1000 genomes]
rs59264464	0.93[ASN][1000 genomes]
rs59412192	0.93[ASN][1000 genomes]
rs59761994	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60677957	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62136987	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62137001	0.88[ASN][1000 genomes]
rs62137002	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62137003	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62137005	0.88[ASN][1000 genomes]
rs62137006	0.88[ASN][1000 genomes]
rs62137007	0.88[ASN][1000 genomes]
rs62137008	0.85[ASN][1000 genomes]
rs62137009	0.85[ASN][1000 genomes]
rs62138801	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545027	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545028	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6545029	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545030	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545034	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545035	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545036	0.83[ASW][hapmap];0.92[CEU][hapmap];0.93[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes]
rs6705802	0.86[JPT][hapmap];0.95[LWK][hapmap]
rs6712029	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6718068	0.86[JPT][hapmap]
rs6743757	0.92[CEU][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs6757206	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72818493	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820405	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72887649	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7340322	0.87[ASN][1000 genomes]
rs7562069	0.85[CEU][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs7562816	0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7566239	0.86[JPT][hapmap]
rs7568960	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7574125	0.81[ASN][1000 genomes]
rs7576964	0.81[JPT][hapmap]
rs7577237	0.86[JPT][hapmap]
rs7579932	0.88[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs7600794	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes]
rs7606104	0.92[CEU][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9309152	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48540600-48547400	Active TSS	GM12878-XiMat	blood
2	chr2:48543200-48553200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:48543400-48545600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:48543400-48546800	Weak transcription	Placenta	Placenta
5	chr2:48543400-48547800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:48543400-48551800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:48543400-48552000	Weak transcription	Stomach Mucosa	stomach
8	chr2:48543400-48553000	Weak transcription	Lung	lung
9	chr2:48543400-48553000	Weak transcription	Psoas Muscle	Psoas
10	chr2:48543400-48568600	Weak transcription	HSMM	muscle
11	chr2:48543600-48545600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:48543600-48545600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:48543600-48546800	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr2:48543600-48547600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:48543600-48548000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:48543600-48548000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:48543600-48548200	Enhancers	Primary hematopoietic stem cells	blood
18	chr2:48543600-48548200	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr2:48543600-48548400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:48543600-48549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:48543600-48550000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr2:48543600-48550200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:48543600-48551000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr2:48543600-48552000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:48543600-48552200	Weak transcription	Osteobl	bone
26	chr2:48543600-48553200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:48543600-48553400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:48543600-48554400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:48543600-48555400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:48543600-48556600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:48543600-48559400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:48543600-48561000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:48543600-48570600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:48543800-48545800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:48543800-48546800	Enhancers	Brain Substantia Nigra	brain
36	chr2:48543800-48550000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:48544000-48545800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:48544000-48546400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr2:48544000-48546600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:48544000-48546800	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr2:48544000-48549800	Enhancers	Primary B cells from peripheral blood	blood
42	chr2:48544000-48550000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr2:48544200-48545800	Enhancers	Primary T cells fromperipheralblood	blood
44	chr2:48544200-48545800	Weak transcription	NHLF	lung
45	chr2:48544200-48547000	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr2:48544200-48549000	Enhancers	Primary B cells from cord blood	blood
47	chr2:48544200-48549400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:48544200-48550000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:48544200-48559600	Weak transcription	Fetal Kidney	kidney
50	chr2:48544400-48545600	Weak transcription	Brain Cingulate Gyrus	brain

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