Variant report

Variant	rs13408188
Chromosome Location	chr2:64335650-64335651
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64331549..64334048-chr2:64335542..64337218,2	K562	blood:
2	chr2:64330755..64332591-chr2:64333598..64336493,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10165165	0.81[ASN][1000 genomes]
rs10169847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170224	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176596	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10183513	0.81[ASN][1000 genomes]
rs10191854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192104	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10192378	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10201191	0.84[AMR][1000 genomes]
rs10204631	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13385515	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13412068	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418461	0.81[ASN][1000 genomes]
rs13419918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428357	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017834	0.84[YRI][hapmap]
rs28757314	0.81[ASN][1000 genomes]
rs28798530	0.81[ASN][1000 genomes]
rs3731962	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671082	0.84[YRI][hapmap]
rs56028117	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56301411	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60338887	0.93[ASN][1000 genomes]
rs60882934	1.00[ASN][1000 genomes]
rs717382	0.84[YRI][hapmap]
rs7579828	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7604199	0.84[YRI][hapmap]

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	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34698	chr2:64312142-64521366	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv34955	chr2:64312182-64521290	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv834243	chr2:64316514-64476935	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64313200-64341800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:64318800-64336400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:64320400-64339200	Weak transcription	NHLF	lung
4	chr2:64322200-64336200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:64322400-64336000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:64322800-64335800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:64323400-64341400	Weak transcription	Aorta	Aorta
8	chr2:64323600-64336000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:64323600-64336000	Weak transcription	Brain Angular Gyrus	brain
10	chr2:64323600-64336000	Weak transcription	Psoas Muscle	Psoas
11	chr2:64323600-64341800	Weak transcription	Right Ventricle	heart
12	chr2:64323600-64364400	Weak transcription	Fetal Brain Male	brain
13	chr2:64323800-64341000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:64323800-64341600	Weak transcription	Gastric	stomach
15	chr2:64323800-64341600	Weak transcription	K562	blood
16	chr2:64324000-64336000	Weak transcription	Dnd41	blood
17	chr2:64324000-64341200	Weak transcription	HSMM	muscle
18	chr2:64324000-64341600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:64324400-64335800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:64324400-64335800	Weak transcription	Brain Substantia Nigra	brain
21	chr2:64324400-64336000	Weak transcription	Ovary	ovary
22	chr2:64324400-64336000	Weak transcription	Spleen	Spleen
23	chr2:64324400-64338200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:64324400-64341600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:64324400-64344800	Weak transcription	HSMMtube	muscle
26	chr2:64325000-64341600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr2:64328800-64336000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr2:64329000-64338800	Weak transcription	Fetal Lung	lung
29	chr2:64329000-64342800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:64329200-64341000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:64329400-64336000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:64329800-64336000	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:64329800-64340200	Genic enhancers	GM12878-XiMat	blood
34	chr2:64330000-64336200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr2:64330200-64336000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
36	chr2:64330400-64336000	Weak transcription	Lung	lung
37	chr2:64330600-64336000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:64330800-64335800	Strong transcription	Fetal Thymus	thymus
39	chr2:64330800-64336000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr2:64330800-64336200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr2:64332200-64340600	Weak transcription	NH-A	brain
42	chr2:64332600-64336000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:64332600-64341000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:64332800-64336400	Strong transcription	Fetal Stomach	stomach
45	chr2:64332800-64338800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:64333000-64335800	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr2:64333000-64335800	Strong transcription	Thymus	Thymus
48	chr2:64333400-64335800	Weak transcription	HMEC	breast
49	chr2:64333400-64336000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:64333400-64336000	Weak transcription	Stomach Smooth Muscle	stomach

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