Variant report

Variant	rs12662536
Chromosome Location	chr6:33635407-33635408
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33604565..33606650-chr6:33635359..33638294,2	K562	blood:
2	chr6:33634324..33636697-chr6:33642308..33645021,2	MCF-7	breast:
3	chr6:33628674..33633402-chr6:33634889..33637916,6	MCF-7	breast:
4	chr6:33623872..33628631-chr6:33630927..33635524,5	K562	blood:
5	chr6:33627824..33631151-chr6:33635216..33637671,3	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1408711	0.81[JPT][hapmap]
rs1570759	0.95[JPT][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs2229634	0.81[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2274198	0.82[EUR][1000 genomes]
rs2296336	0.81[CEU][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2296337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296340	1.00[ASW][hapmap]
rs2296343	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6901411	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6908236	0.83[CHD][hapmap]
rs9368771	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9394158	0.81[JPT][hapmap]

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	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv470811	chr6:33622933-33647651	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv602838	chr6:33624733-33650743	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv885771	chr6:33626717-33660143	Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12662536	STK38	cis	parietal	SCAN
rs12662536	RPL10A	cis	parietal	SCAN
rs12662536	C6orf126	cis	cerebellum	SCAN
rs12662536	SPDEF	cis	cerebellum	SCAN
rs12662536	ITPR3	cis	multi-tissue	Pritchard

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33602400-33636400	Weak transcription	HSMMtube	muscle
2	chr6:33603400-33640400	Weak transcription	HUVEC	blood vessel
3	chr6:33603400-33641200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:33605200-33636400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:33606800-33646600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:33608200-33640800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:33611400-33643400	Weak transcription	Left Ventricle	heart
8	chr6:33613000-33659400	Strong transcription	Fetal Intestine Small	intestine
9	chr6:33613200-33660400	Strong transcription	Thymus	Thymus
10	chr6:33614400-33636200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr6:33615000-33660800	Strong transcription	Fetal Intestine Large	intestine
12	chr6:33619600-33660800	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr6:33621000-33659400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr6:33621200-33636200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr6:33621200-33636400	Strong transcription	Primary T cells from cord blood	blood
16	chr6:33621200-33636400	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:33621400-33635800	Strong transcription	Colonic Mucosa	Colon
18	chr6:33621400-33636400	Strong transcription	Lung	lung
19	chr6:33621400-33643400	Strong transcription	Spleen	Spleen
20	chr6:33621400-33662200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:33621400-33672600	Strong transcription	Dnd41	blood
22	chr6:33622000-33660000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:33622400-33644400	Strong transcription	Gastric	stomach
24	chr6:33623200-33635600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:33623200-33636200	Strong transcription	HMEC	breast
26	chr6:33623200-33649000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr6:33623400-33641000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:33623400-33644000	Strong transcription	Fetal Stomach	stomach
29	chr6:33624200-33636200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:33624200-33639200	Strong transcription	NHLF	lung
31	chr6:33624600-33635800	Weak transcription	HepG2	liver
32	chr6:33624600-33664800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr6:33624800-33639400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:33625200-33645200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr6:33625600-33636200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr6:33625800-33635600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:33626000-33638600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:33626600-33636000	Weak transcription	K562	blood
39	chr6:33626600-33638800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:33627200-33636000	Weak transcription	Fetal Lung	lung
41	chr6:33628800-33636600	Strong transcription	NHDF-Ad	bronchial
42	chr6:33629000-33662800	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:33630200-33651000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr6:33630400-33636200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr6:33630400-33636400	Strong transcription	Esophagus	oesophagus
46	chr6:33630400-33640000	Strong transcription	Muscle Satellite Cultured Cells	--
47	chr6:33630400-33650800	Weak transcription	Ovary	ovary
48	chr6:33630400-33660800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr6:33630600-33635800	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr6:33630600-33636200	Strong transcription	Primary T cells fromperipheralblood	blood

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