Variant report

Variant	rs6492725
Chromosome Location	chr13:95285580-95285581
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:95279700..95282385-chr13:95284753..95286898,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1341267	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1572935	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2298055	0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2298056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35253817	0.91[ASN][1000 genomes]
rs3897473	0.90[ASN][1000 genomes]
rs3897474	0.93[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs4238308	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4296139	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4465476	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4771890	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6492720	0.91[ASN][1000 genomes]
rs6492721	0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs6492723	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7326576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7981788	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs9516445	0.90[ASN][1000 genomes]
rs9516448	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs9524555	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs9524556	0.93[ASN][1000 genomes]
rs9524557	1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs9524559	0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs9524561	0.85[JPT][hapmap]
rs9524566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9524568	0.97[ASN][1000 genomes]
rs9556405	0.88[ASN][1000 genomes]
rs9561643	0.85[ASN][1000 genomes]
rs9561645	0.93[ASN][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	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv832686	chr13:95206742-95400992	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6492725	ITR	cis	multi-tissue	Pritchard
rs6492725	UGGT2	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95254800-95288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:95255400-95288600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr13:95260000-95285800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr13:95264200-95299600	Weak transcription	Psoas Muscle	Psoas
5	chr13:95264600-95289200	Weak transcription	Esophagus	oesophagus
6	chr13:95264600-95289600	Weak transcription	Fetal Kidney	kidney
7	chr13:95265400-95286800	Weak transcription	A549	lung
8	chr13:95265600-95293400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr13:95275800-95288800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr13:95276600-95292800	Weak transcription	Colon Smooth Muscle	Colon
11	chr13:95276600-95293600	Weak transcription	HSMMtube	muscle
12	chr13:95276800-95286000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr13:95276800-95286200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr13:95276800-95287000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr13:95276800-95287400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr13:95276800-95288600	Weak transcription	Primary T cells from cord blood	blood
17	chr13:95276800-95288800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr13:95276800-95289000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr13:95276800-95292400	Weak transcription	NHEK	skin
20	chr13:95276800-95292800	Weak transcription	NHLF	lung
21	chr13:95276800-95294000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr13:95277000-95286200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr13:95277000-95289200	Weak transcription	Brain Hippocampus Middle	brain
24	chr13:95277200-95287600	Weak transcription	Fetal Brain Female	brain
25	chr13:95277200-95291200	Weak transcription	Primary B cells from cord blood	blood
26	chr13:95277200-95293000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr13:95277400-95285600	Weak transcription	Fetal Intestine Small	intestine
28	chr13:95277400-95287600	Weak transcription	Fetal Stomach	stomach
29	chr13:95277400-95289800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr13:95277400-95293400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr13:95277400-95293800	Weak transcription	Ovary	ovary
32	chr13:95277800-95293200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr13:95278800-95289200	Weak transcription	Fetal Intestine Large	intestine
34	chr13:95279400-95287600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr13:95279600-95289200	Weak transcription	Brain Anterior Caudate	brain
36	chr13:95279800-95289000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr13:95280600-95286000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr13:95280600-95293000	Weak transcription	HUVEC	blood vessel
39	chr13:95280600-95293600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr13:95281200-95286800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr13:95281200-95287000	Weak transcription	NHDF-Ad	bronchial
42	chr13:95282200-95286200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr13:95282200-95289000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr13:95282400-95287200	Weak transcription	HMEC	breast
45	chr13:95282400-95292800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr13:95282600-95287200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr13:95282600-95287200	Weak transcription	HSMM	muscle
48	chr13:95282800-95293400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr13:95283000-95287200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr13:95283000-95289200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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