Variant report

Variant	rs4304397
Chromosome Location	chr9:115598154-115598155
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	chr9:115511814..115513808-chr9:115597471..115599757,2	MCF-7	breast:
2	chr9:115581292..115584107-chr9:115597875..115599534,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226609	Chromatin interaction
ENSG00000148158	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10115576	0.85[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap]
rs10124260	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10124939	0.88[GIH][hapmap]
rs10733594	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10733598	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs10733599	0.85[CEU][hapmap]
rs10739370	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10739373	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10739374	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10739376	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs10739378	0.85[CEU][hapmap]
rs10759584	0.86[EUR][1000 genomes]
rs10759590	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs10759603	0.85[CEU][hapmap]
rs1324931	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs1361719	0.84[EUR][1000 genomes]
rs1361720	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1418409	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1418410	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs1475293	0.85[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap]
rs1539338	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1711739	0.85[CEU][hapmap]
rs1711744	0.83[TSI][hapmap]
rs1711745	0.82[CEU][hapmap]
rs1711746	0.82[CEU][hapmap]
rs1711747	0.86[GIH][hapmap];0.88[TSI][hapmap]
rs1891402	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1891403	1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap]
rs2025544	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap]
rs2153837	0.85[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap]
rs2185769	0.85[CEU][hapmap]
rs2645991	0.82[EUR][1000 genomes]
rs2645993	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2645994	0.85[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs2796025	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2796028	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs2796031	0.82[EUR][1000 genomes]
rs4246892	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4549852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4604521	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4978507	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4978511	0.88[GIH][hapmap]
rs4979148	0.86[EUR][1000 genomes]
rs4979150	0.86[EUR][1000 genomes]
rs4979153	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4979154	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4979155	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4979157	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4979165	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4979170	0.85[CEU][hapmap]
rs6477959	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs700122	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7030795	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7038684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7041965	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7047914	0.84[EUR][1000 genomes]
rs7859175	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7868830	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs786961	1.00[ASW][hapmap];0.85[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap]
rs786966	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs786968	0.87[GIH][hapmap];0.88[TSI][hapmap]
rs786977	0.87[GIH][hapmap];0.88[TSI][hapmap]
rs786978	0.83[TSI][hapmap]
rs7872308	0.84[EUR][1000 genomes]
rs7872628	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs787271	1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs787274	0.88[GIH][hapmap]
rs787276	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs787278	0.85[CEU][hapmap]
rs787279	0.86[EUR][1000 genomes]
rs787280	1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs787281	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs787284	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs787285	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs787286	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs787287	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs787294	1.00[CEU][hapmap]
rs787295	1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs787296	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs787297	1.00[CEU][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs787298	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs787299	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs787301	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs787302	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs787303	0.90[AFR][1000 genomes]
rs7873289	0.85[CEU][hapmap]
rs813101	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs885387	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9409123	1.00[CEU][hapmap]
rs947609	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4304397	TSCOT	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115559400-115598400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr9:115565000-115600800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr9:115565600-115600800	Weak transcription	HMEC	breast
4	chr9:115570600-115608400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:115573200-115598400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:115573400-115598800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:115573600-115598400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:115573600-115607800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:115574000-115598600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr9:115575000-115600800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr9:115577600-115630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr9:115579000-115600800	Weak transcription	Fetal Brain Male	brain
13	chr9:115580200-115608400	Weak transcription	Fetal Kidney	kidney
14	chr9:115580600-115601800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:115581200-115598600	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr9:115581200-115599200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr9:115582200-115608600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr9:115582400-115598200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr9:115582400-115598400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr9:115582400-115600600	Weak transcription	HSMM	muscle
21	chr9:115582400-115608600	Weak transcription	NHLF	lung
22	chr9:115582400-115609000	Weak transcription	NHDF-Ad	bronchial
23	chr9:115582400-115630000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr9:115582600-115598600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:115583400-115598200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:115583400-115598200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:115583600-115598400	Weak transcription	NHEK	skin
28	chr9:115584400-115608800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr9:115587000-115598200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:115587200-115598600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr9:115591200-115606800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr9:115591400-115623200	Weak transcription	Fetal Heart	heart
33	chr9:115592400-115600000	Weak transcription	Dnd41	blood
34	chr9:115592600-115607200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr9:115593200-115598200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:115593200-115611000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr9:115593400-115602600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr9:115593600-115599600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:115593600-115607200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr9:115593800-115599000	Weak transcription	Primary B cells from cord blood	blood
41	chr9:115594000-115598200	Weak transcription	Right Ventricle	heart
42	chr9:115594000-115602800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:115594200-115598400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr9:115594200-115598400	Weak transcription	Aorta	Aorta
45	chr9:115594200-115598400	Weak transcription	Pancreas	Pancrea
46	chr9:115594200-115598400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr9:115594200-115598600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr9:115594200-115598600	Weak transcription	Left Ventricle	heart
49	chr9:115594200-115598600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr9:115594200-115598800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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