Variant report

Variant	rs6478118
Chromosome Location	chr9:117673146-117673147
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:117443850..117445001-chr9:117673133..117675031,14	MCF-7	breast:
2	chr9:117423941..117424774-chr9:117672688..117673402,2	MCF-7	breast:
3	chr9:117500823..117501813-chr9:117672459..117674068,13	MCF-7	breast:
4	chr9:117672786..117673783-chr9:117775999..117776990,4	MCF-7	breast:
5	chr9:117424187..117425031-chr9:117672821..117673695,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230054	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10817681	0.92[AFR][1000 genomes]
rs10982448	0.85[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs16931962	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1885383	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2181032	0.93[ASN][1000 genomes]
rs3181194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3181346	0.96[YRI][hapmap]
rs3181349	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs3181350	0.87[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs3181357	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3181359	0.86[AFR][1000 genomes]
rs3181360	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3181362	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3789882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3827818	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs4978612	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61024439	0.86[AFR][1000 genomes]
rs7854103	0.86[AFR][1000 genomes]
rs7868670	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7871914	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs973351	0.85[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	nsv831695	chr9:117567626-117726247	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv893767	chr9:117627569-117689838	Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117662200-117676200	Weak transcription	Gastric	stomach
2	chr9:117667400-117673600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr9:117667600-117673200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:117667800-117683600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr9:117668800-117673400	Enhancers	Primary B cells from peripheral blood	blood
6	chr9:117668800-117673400	Enhancers	HMEC	breast
7	chr9:117669000-117674000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr9:117669200-117673200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr9:117669200-117673800	Enhancers	Fetal Thymus	thymus
10	chr9:117669800-117673600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr9:117670200-117673600	Enhancers	Osteobl	bone
12	chr9:117670400-117673400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:117670800-117673800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr9:117670800-117674200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr9:117670800-117687200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:117671000-117673200	Genic enhancers	Primary T cells from cord blood	blood
17	chr9:117671000-117674600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr9:117671200-117674200	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr9:117671200-117676800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:117671400-117673200	Weak transcription	NHLF	lung
21	chr9:117671400-117674000	Enhancers	Hela-S3	cervix
22	chr9:117671400-117674200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr9:117671600-117673200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:117671600-117673400	Weak transcription	NH-A	brain
25	chr9:117671600-117674000	Enhancers	A549	lung
26	chr9:117671600-117675000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr9:117671800-117673200	Genic enhancers	Thymus	Thymus
28	chr9:117671800-117674800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr9:117671800-117676600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr9:117671800-117676800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr9:117672000-117674400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
32	chr9:117672000-117674400	Enhancers	Dnd41	blood
33	chr9:117672200-117673200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:117672200-117673200	Weak transcription	Fetal Lung	lung
35	chr9:117672200-117673400	Enhancers	Fetal Muscle Leg	muscle
36	chr9:117672200-117673600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr9:117672200-117676600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr9:117672400-117673600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:117672400-117673800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:117672400-117681600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr9:117672600-117673400	Enhancers	Rectal Smooth Muscle	rectum
42	chr9:117672600-117673600	Enhancers	Brain Anterior Caudate	brain
43	chr9:117672600-117673600	Enhancers	HSMM	muscle
44	chr9:117672600-117675000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr9:117672800-117673200	Enhancers	Esophagus	oesophagus
46	chr9:117672800-117673200	Enhancers	Fetal Brain Female	brain
47	chr9:117672800-117673200	Enhancers	Spleen	Spleen
48	chr9:117672800-117673200	Genic enhancers	Monocytes-CD14+_RO01746	blood
49	chr9:117672800-117673400	Enhancers	Colon Smooth Muscle	Colon
50	chr9:117672800-117673400	Enhancers	HSMMtube	muscle

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