Variant report

Variant	rs4979176
Chromosome Location	chr9:115641181-115641182
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115639836..115642850-chr9:115645112..115647078,3	MCF-7	breast:
2	chr9:115634993..115639011-chr9:115640065..115646725,6	MCF-7	breast:
3	chr9:115636020..115638444-chr9:115640356..115642230,2	K562	blood:
4	chr9:115636547..115639081-chr9:115640753..115642299,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10114602	0.87[EUR][1000 genomes]
rs10114623	0.87[EUR][1000 genomes]
rs10115576	1.00[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs10115711	0.82[CEU][hapmap]
rs10116897	0.87[EUR][1000 genomes]
rs10124260	0.85[CEU][hapmap]
rs10124939	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[ASN][1000 genomes]
rs10124979	0.82[CEU][hapmap]
rs1041086	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10733594	0.85[CEU][hapmap]
rs10733598	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10733599	1.00[CEU][hapmap]
rs10739370	0.82[CEU][hapmap]
rs10739373	0.85[CEU][hapmap];0.94[GIH][hapmap];0.82[TSI][hapmap]
rs10739376	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10739377	0.87[EUR][1000 genomes]
rs10739378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739380	0.89[ASN][1000 genomes]
rs10759590	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10759603	1.00[CEU][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10759604	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10981534	0.87[EUR][1000 genomes]
rs1324930	0.87[EUR][1000 genomes]
rs1324931	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1324932	0.87[EUR][1000 genomes]
rs1361720	0.85[CEU][hapmap]
rs1418409	0.85[CEU][hapmap]
rs1475293	1.00[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs1539338	0.85[CEU][hapmap]
rs1711747	0.81[GIH][hapmap]
rs1891402	0.85[CEU][hapmap]
rs1891403	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs2025544	1.00[CEU][hapmap];0.94[GIH][hapmap]
rs2645993	0.85[CEU][hapmap]
rs2645994	0.82[GIH][hapmap]
rs2796028	0.85[CEU][hapmap]
rs4246892	0.85[CEU][hapmap]
rs4304397	0.85[CEU][hapmap];0.94[GIH][hapmap]
rs4978507	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs4978509	0.87[EUR][1000 genomes]
rs4978511	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[ASN][1000 genomes]
rs4979153	0.85[CEU][hapmap]
rs4979154	0.85[CEU][hapmap]
rs4979157	0.85[CEU][hapmap]
rs4979165	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs4979170	1.00[CEU][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.94[EUR][1000 genomes]
rs4979173	0.94[EUR][1000 genomes]
rs4979175	0.87[EUR][1000 genomes]
rs4979177	0.92[EUR][1000 genomes]
rs4979178	0.92[EUR][1000 genomes]
rs62576453	0.86[EUR][1000 genomes]
rs6477959	0.85[CEU][hapmap]
rs700122	0.85[CEU][hapmap]
rs7023956	0.82[EUR][1000 genomes]
rs7030795	0.85[CEU][hapmap]
rs7047914	0.92[EUR][1000 genomes]
rs7859175	0.85[CEU][hapmap]
rs7868830	0.85[CEU][hapmap]
rs786961	0.82[GIH][hapmap]
rs786966	0.82[GIH][hapmap]
rs786968	0.82[GIH][hapmap]
rs786977	0.82[GIH][hapmap]
rs787271	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs787274	0.83[GIH][hapmap]
rs787276	0.85[CEU][hapmap]
rs787280	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs787284	0.85[CEU][hapmap]
rs787287	0.85[CEU][hapmap]
rs787294	0.85[CEU][hapmap]
rs787295	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs787297	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs787298	0.85[CEU][hapmap]
rs787299	0.85[CEU][hapmap];0.94[GIH][hapmap];0.82[TSI][hapmap]
rs787301	0.85[CEU][hapmap];0.81[GIH][hapmap]
rs787302	0.85[CEU][hapmap]
rs7873289	1.00[CEU][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs813101	0.85[CEU][hapmap]
rs885387	0.85[CEU][hapmap]
rs9409123	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4979176	JUP	trans	lymphoblastoid	seeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115601200-115641200	Weak transcription	Fetal Brain Male	brain
2	chr9:115607400-115643400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:115613600-115642600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:115615600-115646400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:115624200-115652600	Weak transcription	Fetal Heart	heart
6	chr9:115625800-115645200	Weak transcription	Thymus	Thymus
7	chr9:115626400-115650800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:115627000-115647000	Weak transcription	Colonic Mucosa	Colon
9	chr9:115627600-115642000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr9:115627600-115646800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr9:115630600-115642000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:115630600-115643400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr9:115630600-115646400	Weak transcription	Fetal Lung	lung
14	chr9:115630600-115647200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:115630800-115643400	Weak transcription	NHEK	skin
16	chr9:115630800-115643600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:115630800-115643600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:115630800-115646400	Weak transcription	Placenta	Placenta
19	chr9:115631200-115643600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:115631200-115646400	Weak transcription	Fetal Kidney	kidney
21	chr9:115631400-115643800	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:115631600-115642800	Weak transcription	Ovary	ovary
23	chr9:115631800-115642800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:115631800-115642800	Weak transcription	HSMM	muscle
25	chr9:115631800-115646400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:115631800-115652200	Weak transcription	Gastric	stomach
27	chr9:115632000-115642600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr9:115632200-115644800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr9:115632400-115643200	Weak transcription	HSMMtube	muscle
30	chr9:115632800-115643400	Weak transcription	HMEC	breast
31	chr9:115633000-115645800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr9:115633000-115646400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr9:115633000-115652600	Weak transcription	Left Ventricle	heart
34	chr9:115633200-115641200	Weak transcription	HepG2	liver
35	chr9:115633200-115642800	Weak transcription	Brain Anterior Caudate	brain
36	chr9:115633200-115646400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr9:115633200-115652400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr9:115633200-115652400	Weak transcription	Right Ventricle	heart
39	chr9:115633400-115643400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:115633400-115643600	Weak transcription	Pancreas	Pancrea
41	chr9:115633400-115646800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr9:115633400-115648200	Weak transcription	Esophagus	oesophagus
43	chr9:115633400-115649200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr9:115633600-115644400	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr9:115633800-115641600	Weak transcription	Brain Substantia Nigra	brain
46	chr9:115633800-115643600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr9:115633800-115652600	Weak transcription	Liver	Liver
48	chr9:115634200-115642600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr9:115634200-115642600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:115634600-115643000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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