Variant report

Variant	rs6479313
Chromosome Location	chr9:108126305-108126306
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108124822..108127933-chr9:108132017..108134314,3	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10123494	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10820801	0.94[ASW][hapmap];0.92[CEU][hapmap];0.96[GIH][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10991629	0.92[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10991639	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12339823	0.84[AMR][1000 genomes]
rs12342542	0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs12344130	0.83[YRI][hapmap]
rs12350138	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs13294525	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13294539	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1410839	0.92[CEU][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16924530	0.83[YRI][hapmap];0.86[AMR][1000 genomes]
rs2417615	0.92[CEU][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2771033	0.92[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2771040	0.92[CEU][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3199966	0.80[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs34750132	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35603631	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4549843	1.00[ASW][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479311	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6479314	0.91[CEU][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479315	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479316	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024985	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7029443	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7044901	1.00[ASN][1000 genomes]
rs7045091	0.92[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7865985	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7873937	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs907230	0.92[CEU][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][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	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6479313	OR13F1	cis	parietal	SCAN
rs6479313	ZNF189	cis	cerebellum	SCAN
rs6479313	CYLC2	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108055600-108151200	Weak transcription	Esophagus	oesophagus
2	chr9:108091600-108150400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:108092000-108148000	Weak transcription	Psoas Muscle	Psoas
4	chr9:108093200-108149800	Weak transcription	HUVEC	blood vessel
5	chr9:108096200-108164200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:108096400-108131800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr9:108097400-108133600	Weak transcription	Placenta	Placenta
8	chr9:108097600-108147000	Weak transcription	HMEC	breast
9	chr9:108100200-108136200	Weak transcription	Fetal Muscle Leg	muscle
10	chr9:108100200-108149600	Weak transcription	Pancreas	Pancrea
11	chr9:108104800-108129600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr9:108104800-108147600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:108105000-108129800	Weak transcription	Ovary	ovary
14	chr9:108105000-108133000	Weak transcription	Dnd41	blood
15	chr9:108105000-108133400	Weak transcription	Fetal Thymus	thymus
16	chr9:108105000-108149600	Weak transcription	Right Ventricle	heart
17	chr9:108105000-108151200	Weak transcription	Gastric	stomach
18	chr9:108105000-108154800	Weak transcription	Small Intestine	intestine
19	chr9:108105200-108149800	Weak transcription	NHDF-Ad	bronchial
20	chr9:108116200-108127800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:108117000-108146400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr9:108117400-108147400	Weak transcription	Spleen	Spleen
23	chr9:108117600-108130000	Weak transcription	Hela-S3	cervix
24	chr9:108118200-108147200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr9:108118400-108134400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr9:108118400-108134400	Strong transcription	Liver	Liver
27	chr9:108118400-108139800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:108118600-108147600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr9:108120000-108129400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr9:108120200-108128000	Strong transcription	Brain Anterior Caudate	brain
31	chr9:108120200-108133600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr9:108120200-108146200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:108121400-108139400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:108121600-108132200	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr9:108121600-108157000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr9:108121800-108137000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr9:108121800-108137000	Weak transcription	Colon Smooth Muscle	Colon
38	chr9:108121800-108148600	Weak transcription	A549	lung
39	chr9:108122000-108127000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr9:108122000-108127000	Strong transcription	Fetal Lung	lung
41	chr9:108122000-108137400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr9:108122200-108132400	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr9:108122200-108133800	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr9:108122200-108134400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:108122400-108126400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:108122400-108127200	Strong transcription	Left Ventricle	heart
47	chr9:108122400-108128600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr9:108122400-108148200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr9:108122600-108127800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr9:108122600-108137400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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