Variant report

Variant	rs643531
Chromosome Location	chr9:15296034-15296035
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15293831..15297894-chr9:15305171..15308300,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155158	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10120504	1.00[JPT][hapmap]
rs10122040	1.00[JPT][hapmap]
rs10122202	1.00[JPT][hapmap]
rs10125329	1.00[JPT][hapmap]
rs10810369	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10961950	1.00[JPT][hapmap]
rs10961951	1.00[JPT][hapmap]
rs10961955	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10962043	1.00[CHB][hapmap]
rs12003180	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs1215112	0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1475229	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16933318	1.00[CHB][hapmap]
rs2156109	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2185938	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2616751	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3901749	1.00[JPT][hapmap]
rs3933784	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3933785	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs4237138	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs471364	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs486349	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540885	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570524	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578194	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581080	0.82[CEU][hapmap]
rs585002	0.82[CEU][hapmap]
rs612183	0.82[JPT][hapmap]
rs660686	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs661048	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs675849	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs677578	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs686030	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7035671	0.82[JPT][hapmap]
rs7035801	0.82[JPT][hapmap]
rs7037559	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7873299	1.00[JPT][hapmap]
rs9657588	1.00[JPT][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	nsv1031340	chr9:15163004-15332769	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2761505	chr9:15274373-15319613	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv2762797	chr9:15282415-15297028	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv892624	chr9:15283761-15415461	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats 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	23 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
HDL cholesterol	20864672	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs643531	TUBGCP6	trans	parietal	SCAN
rs643531	MPDZ	cis	parietal	SCAN
rs643531	C9orf52	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15277600-15296800	Weak transcription	Gastric	stomach
2	chr9:15287400-15303600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:15290800-15305600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:15290800-15306000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:15291200-15305600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:15292200-15296800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:15293400-15296400	Enhancers	Fetal Intestine Large	intestine
8	chr9:15294200-15296600	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr9:15294400-15306200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:15294600-15297600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr9:15294800-15297000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:15294800-15297200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:15294800-15297600	Enhancers	Lung	lung
14	chr9:15295000-15296800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:15295000-15297000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr9:15295200-15296200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr9:15295200-15297800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr9:15295400-15296800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:15295400-15297200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:15295400-15297200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:15295400-15297200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:15295400-15297400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:15295600-15296200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr9:15295600-15296200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:15295600-15296200	Flanking Active TSS	Liver	Liver
26	chr9:15295600-15296200	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr9:15295600-15296200	Flanking Active TSS	HUVEC	blood vessel
28	chr9:15295600-15296200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr9:15295600-15296600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr9:15295600-15296600	Flanking Active TSS	GM12878-XiMat	blood
31	chr9:15295600-15297400	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr9:15295800-15296200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:15295800-15296200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr9:15295800-15296200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr9:15295800-15296200	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr9:15295800-15296200	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr9:15295800-15296200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr9:15295800-15296200	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr9:15295800-15296200	Active TSS	Fetal Brain Male	brain
40	chr9:15295800-15296200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr9:15295800-15296200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr9:15295800-15296200	Flanking Active TSS	HMEC	breast
43	chr9:15295800-15296200	Flanking Active TSS	NHEK	skin
44	chr9:15295800-15296400	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr9:15295800-15296400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr9:15295800-15296400	Flanking Active TSS	HepG2	liver
47	chr9:15295800-15296600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr9:15295800-15296600	Flanking Active TSS	Fetal Kidney	kidney
49	chr9:15295800-15296800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
50	chr9:15295800-15296800	Flanking Active TSS	Fetal Thymus	thymus

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