Variant report

Variant	rs13017699
Chromosome Location	chr2:30376345-30376346
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:30376051-30376712	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:30376221-30377409	A549	lung:	n/a	n/a
3	POLR2A	chr2:30376147-30376659	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30366474..30375732-chr2:30375765..30384167,14	MCF-7	breast:
2	chr2:30375240..30377152-chr2:30455501..30457902,2	K562	blood:

Variant related genes	Relation type
YPEL5	TF binding region
ENSG00000213626	Chromatin interaction
ENSG00000119801	Chromatin interaction
ENSG00000233862	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11127257	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11127258	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1137288	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs11688623	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11690964	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11903016	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12620501	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12991494	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17734800	0.93[ASN][1000 genomes]
rs17734815	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2276548	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2361753	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34125526	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34350694	0.97[ASN][1000 genomes]
rs35466989	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35640159	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4465805	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55869928	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62141084	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62141087	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62141088	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6747196	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7600457	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs7603324	0.89[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription 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	32 gene(s)	inside rSNPs	diseases
2	nsv1002657	chr2:30339312-30516535	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30371000-30380200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:30371000-30380600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:30371400-30380000	Weak transcription	Esophagus	oesophagus
4	chr2:30371400-30380000	Weak transcription	Dnd41	blood
5	chr2:30371400-30380200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:30371400-30384800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:30371600-30380200	Weak transcription	Colonic Mucosa	Colon
8	chr2:30371800-30385000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:30372200-30378800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:30372400-30378400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:30372800-30376600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:30372800-30377400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:30372800-30378600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:30372800-30378600	Weak transcription	Stomach Mucosa	stomach
15	chr2:30372800-30379600	Weak transcription	Fetal Stomach	stomach
16	chr2:30372800-30379600	Weak transcription	Lung	lung
17	chr2:30372800-30380200	Weak transcription	Fetal Brain Male	brain
18	chr2:30373000-30377400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr2:30373000-30379600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:30373200-30378600	Weak transcription	Fetal Kidney	kidney
21	chr2:30373200-30379400	Weak transcription	Brain Angular Gyrus	brain
22	chr2:30373200-30379600	Weak transcription	Brain Anterior Caudate	brain
23	chr2:30373200-30379600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:30373200-30379800	Weak transcription	Fetal Brain Female	brain
25	chr2:30373200-30380200	Weak transcription	Brain Germinal Matrix	brain
26	chr2:30373200-30380400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:30373200-30396400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:30373400-30376800	Weak transcription	Aorta	Aorta
29	chr2:30373400-30378800	Weak transcription	Left Ventricle	heart
30	chr2:30373400-30379200	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:30373400-30380200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:30373400-30381400	Weak transcription	HMEC	breast
33	chr2:30373600-30378800	Weak transcription	NHEK	skin
34	chr2:30373800-30377800	Weak transcription	HUVEC	blood vessel
35	chr2:30373800-30378000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:30373800-30379600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:30373800-30379600	Weak transcription	Fetal Lung	lung
38	chr2:30373800-30380200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:30373800-30380600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:30373800-30385200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr2:30374000-30376600	Strong transcription	Fetal Thymus	thymus
42	chr2:30374000-30377400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:30374000-30377600	Weak transcription	Small Intestine	intestine
44	chr2:30374000-30378000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:30374000-30378200	Weak transcription	A549	lung
46	chr2:30374000-30378400	Weak transcription	HepG2	liver
47	chr2:30374000-30378600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr2:30374000-30378800	Weak transcription	Fetal Intestine Small	intestine
49	chr2:30374000-30378800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:30374000-30379000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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