Variant report

Variant	rs1217339
Chromosome Location	chr9:72047599-72047600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72044312..72045985-chr9:72046714..72048470,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1029066	0.92[CEU][hapmap]
rs10780336	0.82[JPT][hapmap]
rs10867453	0.81[JPT][hapmap]
rs10867655	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10867656	0.81[ASW][hapmap];0.92[CEU][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11138435	0.81[JPT][hapmap]
rs1217338	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1234632	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1330329	0.92[CEU][hapmap]
rs1331973	0.92[CEU][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1331974	0.88[JPT][hapmap]
rs1331976	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1331977	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs1757957	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1761285	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1761293	0.84[ASN][1000 genomes]
rs1806760	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1888834	0.92[CEU][hapmap]
rs2150878	0.92[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2253885	0.92[ASW][hapmap];0.81[YRI][hapmap]
rs2777862	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2777863	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2777865	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2781533	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2781535	0.88[ASN][1000 genomes]
rs2991694	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991695	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737172	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3737175	0.95[ASN][1000 genomes]
rs4316205	0.81[AFR][1000 genomes]
rs4492445	0.82[JPT][hapmap]
rs4744569	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs6559613	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7019125	0.84[CEU][hapmap];0.84[YRI][hapmap]
rs7021184	0.84[CHD][hapmap];0.88[JPT][hapmap]
rs7024302	0.81[JPT][hapmap]
rs7035141	0.81[JPT][hapmap]
rs7049022	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72717108	0.99[ASN][1000 genomes]
rs7850597	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7858171	0.92[CEU][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs7866199	0.92[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7872660	0.92[CEU][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs879767	0.92[CEU][hapmap];0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs914551	0.85[CEU][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9410852	0.84[ASN][1000 genomes]
rs9776833	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv893431	chr9:72003036-72048098	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv2757340	chr9:72018246-72048098	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2759694	chr9:72018246-72048098	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv893432	chr9:72028323-72056397	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1047666	chr9:72028458-72049592	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1048650	chr9:72028458-72179847	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv2761289	chr9:72028470-72049604	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1049763	chr9:72029588-72049592	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv2422080	chr9:72029600-72049028	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1045274	chr9:72032381-72049592	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv1048256	chr9:72032381-72067786	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv1045239	chr9:72032381-72067942	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1041436	chr9:72032381-72069314	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	esv3396573	chr9:72033229-72054457	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	esv15039	chr9:72034725-72049025	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	esv2761532	chr9:72035189-72049604	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv442554	chr9:72035193-72049028	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv1038185	chr9:72035199-72057304	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	esv3693030	chr9:72035847-72048477	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv520760	chr9:72035847-72048477	Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
24	nsv818703	chr9:72035847-72048477	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
25	nsv1052872	chr9:72040184-72081554	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
26	nsv1037109	chr9:72040184-72120270	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
27	esv3483549	chr9:72042632-72047730	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72036600-72082600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr9:72037200-72048600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:72037200-72055600	Weak transcription	Fetal Lung	lung
4	chr9:72037200-72056200	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:72040800-72057400	Weak transcription	Fetal Heart	heart
6	chr9:72041200-72069600	Weak transcription	Gastric	stomach
7	chr9:72041600-72049400	Strong transcription	Liver	Liver
8	chr9:72042000-72070400	Weak transcription	Spleen	Spleen
9	chr9:72042600-72048000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:72042800-72063800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:72043200-72063800	Weak transcription	Brain Substantia Nigra	brain
12	chr9:72043400-72055400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:72043400-72055600	Weak transcription	Brain Angular Gyrus	brain
14	chr9:72044200-72084400	Weak transcription	Fetal Intestine Small	intestine
15	chr9:72044800-72048200	Strong transcription	Fetal Stomach	stomach
16	chr9:72045000-72048400	Strong transcription	Brain Hippocampus Middle	brain
17	chr9:72045000-72084400	Weak transcription	Fetal Intestine Large	intestine
18	chr9:72045200-72048200	Strong transcription	Fetal Brain Female	brain
19	chr9:72045400-72048000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr9:72045400-72048400	Strong transcription	Ovary	ovary
21	chr9:72045400-72050600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:72045600-72047800	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:72045800-72048600	Strong transcription	Brain Cingulate Gyrus	brain
24	chr9:72045800-72064200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr9:72046000-72056400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr9:72046200-72047800	ZNF genes & repeats	Aorta	Aorta
27	chr9:72046400-72085600	Weak transcription	Colon Smooth Muscle	Colon
28	chr9:72046600-72048000	Strong transcription	Brain Anterior Caudate	brain
29	chr9:72046600-72049400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:72046800-72047800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr9:72046800-72055600	Weak transcription	Brain Germinal Matrix	brain
32	chr9:72047000-72047800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:72047000-72048200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:72047000-72055600	Weak transcription	Adipose Nuclei	Adipose
35	chr9:72047000-72055600	Weak transcription	Pancreas	Pancrea
36	chr9:72047000-72055600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr9:72047000-72056600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr9:72047000-72056800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr9:72047000-72081800	Weak transcription	Fetal Kidney	kidney
40	chr9:72047200-72055600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr9:72047400-72047800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr9:72047400-72055200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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