Variant report

Variant	rs10840175
Chromosome Location	chr11:9143548-9143549
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	chr11:9113356..9115182-chr11:9141033..9143763,3	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10047438	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1039210	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10769991	0.85[CHD][hapmap]
rs10769992	0.92[CEU][hapmap]
rs10769993	1.00[JPT][hapmap]
rs10769994	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10769997	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10769998	0.82[EUR][1000 genomes]
rs10840174	0.92[ASN][1000 genomes]
rs10840176	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10840183	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10840185	0.83[EUR][1000 genomes]
rs11042189	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042200	0.87[CEU][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11604616	0.81[CHD][hapmap];0.83[MEX][hapmap]
rs12286943	0.88[JPT][hapmap]
rs12290916	0.82[ASN][1000 genomes]
rs12291375	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1353730	0.88[JPT][hapmap]
rs1827011	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1874822	1.00[CEU][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2133217	0.84[CEU][hapmap];0.96[MEX][hapmap];0.86[EUR][1000 genomes]
rs2316087	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2316088	0.88[JPT][hapmap]
rs2647533	0.92[CEU][hapmap]
rs2647537	0.96[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.86[EUR][1000 genomes]
rs2742556	1.00[CEU][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2742557	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3898554	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4910035	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5011703	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7109745	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7120239	0.82[EUR][1000 genomes]
rs7128469	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7394878	0.91[MEX][hapmap]
rs7395151	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7395347	0.85[CHD][hapmap];0.80[AMR][1000 genomes]
rs7395846	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7396705	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7930192	0.88[JPT][hapmap]
rs7930507	0.84[CEU][hapmap];0.96[MEX][hapmap];0.82[EUR][1000 genomes]
rs7931872	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7947251	1.00[CEU][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7948219	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10840175	TRIM5	cis	cerebellum	SCAN
rs10840175	TMEM41B	cis	multi-tissue	Pritchard
rs10840175	EIF4G2	cis	cerebellum	SCAN
rs10840175	OR56A1	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9113600-9159800	Weak transcription	Right Ventricle	heart
2	chr11:9121800-9154800	Weak transcription	Brain Substantia Nigra	brain
3	chr11:9130800-9153600	Weak transcription	Brain Angular Gyrus	brain
4	chr11:9132000-9153200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr11:9134000-9153000	Weak transcription	Brain Germinal Matrix	brain
6	chr11:9134000-9154000	Weak transcription	Osteobl	bone
7	chr11:9134200-9154000	Weak transcription	NHDF-Ad	bronchial
8	chr11:9134800-9159000	Weak transcription	Brain Hippocampus Middle	brain
9	chr11:9134800-9161200	Weak transcription	Fetal Brain Male	brain
10	chr11:9135200-9152600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr11:9135600-9153000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:9136400-9159200	Weak transcription	Brain Anterior Caudate	brain
13	chr11:9137200-9145400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:9137200-9159000	Weak transcription	Fetal Heart	heart
15	chr11:9137800-9146200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:9141200-9144000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr11:9141200-9153000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr11:9141400-9151800	Weak transcription	Psoas Muscle	Psoas
19	chr11:9141400-9153600	Weak transcription	Primary T cells from cord blood	blood
20	chr11:9141400-9153800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr11:9141600-9151800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr11:9141600-9158400	Weak transcription	Pancreas	Pancrea
23	chr11:9141800-9143600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr11:9141800-9143600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr11:9141800-9143800	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr11:9142000-9143600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr11:9142000-9143600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:9142000-9148400	Weak transcription	Right Atrium	heart
29	chr11:9142000-9157200	Weak transcription	NHLF	lung
30	chr11:9142200-9143600	Enhancers	H1 Cell Line	embryonic stem cell
31	chr11:9142400-9143800	Strong transcription	Fetal Stomach	stomach
32	chr11:9142400-9163000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr11:9142600-9143600	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr11:9142600-9143800	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr11:9142600-9153000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:9142600-9159000	Weak transcription	Adipose Nuclei	Adipose
37	chr11:9142600-9159200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr11:9142600-9175000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr11:9142800-9143600	Strong transcription	HSMM	muscle
40	chr11:9142800-9145400	Weak transcription	K562	blood
41	chr11:9142800-9145800	Weak transcription	Fetal Muscle Leg	muscle
42	chr11:9143000-9143600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr11:9143000-9143800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:9143000-9143800	Strong transcription	Fetal Brain Female	brain
45	chr11:9143000-9152600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:9143000-9154400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:9143000-9155000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:9143400-9144200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr11:9143400-9149400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr11:9143400-9152000	Weak transcription	Left Ventricle	heart

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