Variant report

Variant	rs9468839
Chromosome Location	chr6:11308035-11308036
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:11293445..11296108-chr6:11306928..11309267,2	MCF-7	breast:
2	chr6:11230582..11233007-chr6:11307793..11310136,2	MCF-7	breast:
3	chr6:11306910..11309167-chr6:11309172..11312096,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12663156	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12663475	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1883240	1.00[CEU][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs2064111	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs2281063	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4368799	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4713353	0.83[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap]
rs4713396	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6457276	0.86[CHB][hapmap]
rs6918500	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6923444	0.89[JPT][hapmap]
rs7762842	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7765241	0.89[JPT][hapmap]

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	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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11296400-11310200	Weak transcription	Spleen	Spleen
2	chr6:11296400-11310400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:11297000-11310200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr6:11298200-11310400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:11299600-11310600	Weak transcription	Thymus	Thymus
6	chr6:11299800-11314000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:11300200-11310400	Weak transcription	Gastric	stomach
8	chr6:11300200-11310400	Weak transcription	Lung	lung
9	chr6:11305800-11310400	Weak transcription	HepG2	liver
10	chr6:11305800-11319400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:11306000-11319400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:11306200-11313200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:11306200-11318000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:11306400-11318000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:11306400-11319400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr6:11306400-11326800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:11306600-11310600	Weak transcription	Fetal Thymus	thymus
18	chr6:11306600-11318200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr6:11306600-11319200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr6:11306800-11309400	Weak transcription	Primary B cells from cord blood	blood
21	chr6:11306800-11310200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr6:11306800-11310200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr6:11307000-11309400	Weak transcription	Primary T cells from cord blood	blood
24	chr6:11307000-11310200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:11307000-11315400	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr6:11307000-11316400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr6:11307000-11319400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr6:11307200-11308200	Enhancers	NHEK	skin
29	chr6:11307200-11310400	Weak transcription	A549	lung
30	chr6:11307200-11317800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr6:11307400-11308200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:11307400-11308200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:11307400-11308200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:11307400-11309000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr6:11307400-11316400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr6:11307600-11308200	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr6:11307600-11308200	Enhancers	Placenta	Placenta
38	chr6:11307600-11308200	Enhancers	HMEC	breast
39	chr6:11307600-11310400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:11308000-11317800	Weak transcription	GM12878-XiMat	blood

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