Variant report

Variant	rs532492
Chromosome Location	chr6:44419336-44419337
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:44412103..44413730-chr6:44418202..44421080,2	MCF-7	breast:
2	chr6:44410364..44415906-chr6:44416897..44422592,7	K562	blood:
3	chr6:44417252..44422229-chr6:44425424..44429511,4	K562	blood:

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10807300	0.93[CEU][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1293205	0.93[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1293208	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1296018	0.93[CEU][hapmap];0.84[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1952979	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2273667	0.80[JPT][hapmap]
rs2297333	0.81[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap]
rs34264814	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4143678	0.98[GIH][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs4711781	0.81[CEU][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs475426	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs525043	0.93[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs526851	0.82[ASN][1000 genomes]
rs545455	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs548342	0.87[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs557470	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs559035	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs564988	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs566078	0.90[JPT][hapmap]
rs67182313	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6923521	0.93[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6942323	0.81[CEU][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs864127	0.87[CEU][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9395017	0.80[JPT][hapmap]
rs9462985	0.81[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap]
rs9462989	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9472273	0.81[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019145	chr6:44313576-44421440	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv885858	chr6:44385441-44421240	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv885859	chr6:44385441-44422466	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv517370	chr6:44385441-44422689	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv1850024	chr6:44388505-44422689	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs532492	CD2AP	cis	cerebellum	SCAN
rs532492	RUNX2	cis	cerebellum	SCAN
rs532492	GPR115	cis	cerebellum	SCAN
rs532492	CDC5L	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44376800-44424400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:44388400-44424400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:44390200-44420200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr6:44396600-44432800	Weak transcription	Fetal Kidney	kidney
5	chr6:44398600-44419600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:44407800-44419800	Weak transcription	HSMMtube	muscle
7	chr6:44410000-44424400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:44410000-44424400	Weak transcription	Colonic Mucosa	Colon
9	chr6:44410000-44424400	Weak transcription	Spleen	Spleen
10	chr6:44410200-44422200	Weak transcription	Fetal Brain Male	brain
11	chr6:44412000-44425800	Weak transcription	Esophagus	oesophagus
12	chr6:44412200-44424600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:44412200-44424600	Weak transcription	Gastric	stomach
14	chr6:44412400-44424200	Weak transcription	Fetal Intestine Small	intestine
15	chr6:44412600-44424600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:44412800-44419600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:44412800-44419600	Weak transcription	Lung	lung
18	chr6:44412800-44419800	Weak transcription	Aorta	Aorta
19	chr6:44412800-44420000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:44412800-44424600	Weak transcription	Pancreas	Pancrea
21	chr6:44413000-44420200	Weak transcription	Fetal Heart	heart
22	chr6:44413600-44419600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:44413600-44419600	Weak transcription	Fetal Stomach	stomach
24	chr6:44413600-44427600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:44414200-44419400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:44414200-44419600	Weak transcription	Left Ventricle	heart
27	chr6:44414200-44419600	Weak transcription	Ovary	ovary
28	chr6:44414200-44419600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:44414200-44424200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr6:44414200-44424400	Weak transcription	Stomach Mucosa	stomach
31	chr6:44414200-44424600	Weak transcription	Psoas Muscle	Psoas
32	chr6:44414600-44419400	Weak transcription	GM12878-XiMat	blood
33	chr6:44414600-44419800	Weak transcription	HMEC	breast
34	chr6:44414600-44420200	Weak transcription	Brain Angular Gyrus	brain
35	chr6:44415000-44420000	Weak transcription	A549	lung
36	chr6:44415200-44419800	Weak transcription	NH-A	brain
37	chr6:44415600-44419400	Weak transcription	NHLF	lung
38	chr6:44415600-44424200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr6:44415800-44419600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr6:44415800-44424400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr6:44416000-44419400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr6:44416000-44419400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:44416000-44419600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:44416000-44419600	Weak transcription	Colon Smooth Muscle	Colon
45	chr6:44416000-44419600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:44416000-44419600	Weak transcription	Right Ventricle	heart
47	chr6:44416000-44419800	Weak transcription	HUVEC	blood vessel
48	chr6:44416000-44422400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:44416000-44423600	Weak transcription	Brain Germinal Matrix	brain
50	chr6:44416000-44424200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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