Variant report

Variant	rs1539341
Chromosome Location	chr9:115616110-115616111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115615876..115617436-chr9:115625877..115628749,2	MCF-7	breast:
2	chr9:115607502..115609208-chr9:115615429..115617354,2	MCF-7	breast:
3	chr9:115612240..115614238-chr9:115614501..115616948,2	K562	blood:
4	chr9:115615772..115618098-chr9:115620406..115622597,2	K562	blood:
5	chr9:115614764..115617679-chr9:115622672..115625535,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10115576	0.81[LWK][hapmap]
rs10117017	0.80[ASN][1000 genomes]
rs10117709	0.82[ASN][1000 genomes]
rs10122712	0.80[ASN][1000 genomes]
rs10481638	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs10732374	0.87[GIH][hapmap];0.80[ASN][1000 genomes]
rs10733595	0.87[GIH][hapmap];0.80[ASN][1000 genomes]
rs10733596	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10733597	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10739371	0.87[GIH][hapmap]
rs10739375	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10759587	0.80[ASN][1000 genomes]
rs10759588	0.80[ASN][1000 genomes]
rs10759589	0.90[ASN][1000 genomes]
rs10759591	0.90[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10759592	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10759593	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10759595	0.87[ASN][1000 genomes]
rs10759596	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10759597	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10759598	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10759599	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10759600	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10759601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10817396	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10817397	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10817398	1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10817399	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10817400	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10817401	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1418408	0.80[ASN][1000 genomes]
rs1475292	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1539340	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1539342	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1539345	0.80[ASN][1000 genomes]
rs1970527	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1970528	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4366151	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4367629	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4979158	0.80[ASN][1000 genomes]
rs4979162	0.80[ASN][1000 genomes]
rs4979163	0.87[GIH][hapmap];0.82[ASN][1000 genomes]
rs4979164	0.82[ASN][1000 genomes]
rs4979166	0.84[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4979167	1.00[ASN][1000 genomes]
rs4979168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs6477961	0.80[ASN][1000 genomes]
rs7856199	0.87[GIH][hapmap];0.80[ASN][1000 genomes]
rs7871799	0.80[ASN][1000 genomes]
rs7873644	0.80[ASN][1000 genomes]
rs912661	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9299210	0.80[ASN][1000 genomes]
rs9299211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9299212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];1.00[ASN][1000 genomes]
rs999018	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv893733	chr9:115397206-115712068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv2422302	chr9:115550339-115656433	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv2757351	chr9:115600623-115632898	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1047000	chr9:115610445-115884038	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1539341	ZFP37	cis	cerebellum	SCAN
rs1539341	TNFSF15	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115577600-115630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr9:115582400-115630000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr9:115591400-115623200	Weak transcription	Fetal Heart	heart
4	chr9:115594200-115620400	Weak transcription	Thymus	Thymus
5	chr9:115594200-115634400	Weak transcription	NH-A	brain
6	chr9:115594400-115626800	Weak transcription	Colon Smooth Muscle	Colon
7	chr9:115599000-115623200	Weak transcription	Right Ventricle	heart
8	chr9:115599400-115623600	Weak transcription	Right Atrium	heart
9	chr9:115599400-115625200	Weak transcription	Colonic Mucosa	Colon
10	chr9:115601200-115641200	Weak transcription	Fetal Brain Male	brain
11	chr9:115601600-115620600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:115602000-115620600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:115602600-115626600	Weak transcription	Brain Germinal Matrix	brain
14	chr9:115602600-115626800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr9:115604000-115626600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:115604200-115621200	Weak transcription	HepG2	liver
17	chr9:115607400-115643400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:115607600-115620800	Strong transcription	Fetal Intestine Small	intestine
19	chr9:115607600-115630200	Weak transcription	NHEK	skin
20	chr9:115608600-115617000	Strong transcription	Fetal Intestine Large	intestine
21	chr9:115609400-115623200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:115611400-115628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr9:115611400-115634600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr9:115611600-115616800	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr9:115611600-115619000	Weak transcription	Fetal Lung	lung
26	chr9:115611600-115626800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr9:115611600-115630200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr9:115611600-115634200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr9:115611800-115617000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:115611800-115617000	Strong transcription	Stomach Smooth Muscle	stomach
31	chr9:115611800-115630200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr9:115612000-115617000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr9:115612000-115620600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr9:115612000-115634600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr9:115612200-115617000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:115612200-115617400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr9:115612200-115620400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:115612400-115617200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:115612400-115617200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr9:115612600-115616200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr9:115612600-115617600	Strong transcription	Primary T cells from cord blood	blood
42	chr9:115613000-115617200	Strong transcription	Liver	Liver
43	chr9:115613000-115617200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr9:115613000-115617200	Strong transcription	Gastric	stomach
45	chr9:115613000-115617400	Strong transcription	Spleen	Spleen
46	chr9:115613200-115617000	Strong transcription	Adipose Nuclei	Adipose
47	chr9:115613200-115617400	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr9:115613400-115623800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr9:115613600-115625400	Weak transcription	Aorta	Aorta
50	chr9:115613600-115628200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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