Variant report

Variant	rs12215372
Chromosome Location	chr6:11383457-11383458
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	chr6:11382893-11383656	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:11379853-11383656	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11229690..11234119-chr6:11380884..11384431,5	MCF-7	breast:

Variant related genes	Relation type
NEDD9	TF binding region
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1012502	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1013678	0.87[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10947204	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12193099	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12199545	0.96[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12204242	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12208626	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12210644	0.90[EUR][1000 genomes]
rs12215715	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12215894	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13198555	0.92[EUR][1000 genomes]
rs13217274	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1810451	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3798752	0.85[CHB][hapmap];0.83[GIH][hapmap]
rs4276494	0.90[EUR][1000 genomes]
rs4403261	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs4533978	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4632886	0.90[EUR][1000 genomes]
rs4711271	0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4711272	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5019594	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs6916534	0.91[EUR][1000 genomes]
rs6918440	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6919269	0.83[TSI][hapmap]
rs6932496	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7738560	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7768351	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9296000	0.90[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs9348868	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9357127	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9461714	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9469034	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12215372	C6orf218	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11377800-11386600	Weak transcription	HepG2	liver
2	chr6:11382400-11384200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:11382400-11384400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:11382600-11383600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr6:11382600-11383600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:11382600-11383600	Enhancers	Fetal Thymus	thymus
7	chr6:11382600-11384200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:11382600-11384800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:11382600-11386800	Weak transcription	Colonic Mucosa	Colon
10	chr6:11382600-11389400	Weak transcription	Lung	lung
11	chr6:11382600-11392400	Weak transcription	Right Atrium	heart
12	chr6:11382800-11383600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr6:11382800-11383600	Flanking Active TSS	GM12878-XiMat	blood
14	chr6:11382800-11384000	Enhancers	Primary B cells from peripheral blood	blood
15	chr6:11383000-11383600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:11383000-11383600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr6:11383000-11383800	Enhancers	Primary T cells from cord blood	blood
18	chr6:11383000-11383800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:11383000-11383800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr6:11383000-11386800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr6:11383200-11383600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr6:11383200-11383600	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr6:11383200-11383600	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr6:11383200-11383600	Enhancers	Small Intestine	intestine
25	chr6:11383200-11383600	Enhancers	Dnd41	blood
26	chr6:11383200-11383800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr6:11383200-11383800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:11383200-11383800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:11383200-11383800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr6:11383200-11383800	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr6:11383200-11384400	Enhancers	Primary B cells from cord blood	blood
32	chr6:11383200-11388600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:11383200-11390200	Weak transcription	Spleen	Spleen
34	chr6:11383400-11384000	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr6:11383400-11385000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:11383400-11385200	Weak transcription	Aorta	Aorta
37	chr6:11383400-11386600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:11383400-11388000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:11383400-11392600	Weak transcription	Duodenum Mucosa	Duodenum

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