Variant report

Variant	rs10114264
Chromosome Location	chr9:79068627-79068628
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79058598..79061580-chr9:79067952..79069510,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10121699	0.83[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10124695	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10735646	0.83[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10869780	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11144864	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs11144865	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs11788095	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1535845	0.85[EUR][1000 genomes]
rs1961995	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs2002423	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs2377639	0.91[JPT][hapmap]
rs2490572	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap]
rs2490576	0.84[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2490584	0.89[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap]
rs2490586	0.94[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2501920	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2501925	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs2501930	0.85[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs4372070	0.91[JPT][hapmap]
rs4745544	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4745551	0.81[JPT][hapmap]
rs638410	0.80[AMR][1000 genomes]
rs6560519	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6560522	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap]
rs7847608	0.83[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.83[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	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10114264	ZSWIM4	trans	brain	seeQTL
rs10114264	C9orf40	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79063000-79070800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr9:79064600-79071000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr9:79065200-79069200	Enhancers	NHDF-Ad	bronchial
4	chr9:79066200-79071000	Weak transcription	A549	lung
5	chr9:79066600-79070800	Weak transcription	HSMMtube	muscle
6	chr9:79066600-79073600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr9:79066800-79070800	Weak transcription	NH-A	brain
8	chr9:79066800-79071000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr9:79066800-79071200	Weak transcription	HMEC	breast
10	chr9:79067400-79068800	Enhancers	HSMM	muscle
11	chr9:79067400-79069200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:79067400-79069200	Enhancers	Osteobl	bone
13	chr9:79067400-79069400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:79067400-79069400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr9:79067600-79069200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr9:79067800-79069800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:79067800-79071200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr9:79068000-79069600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr9:79068000-79069600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:79068000-79071600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:79068200-79071000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr9:79068200-79071200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr9:79068200-79071400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr9:79068400-79068800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:79068400-79068800	Enhancers	NHLF	lung
26	chr9:79068400-79069600	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr9:79068400-79071000	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr9:79068400-79071000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr9:79068400-79071200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr9:79068600-79068800	Enhancers	Primary hematopoietic stem cells	blood
31	chr9:79068600-79069000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr9:79068600-79069000	Enhancers	Placenta	Placenta
33	chr9:79068600-79069400	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr9:79068600-79071200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:79068600-79073600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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