Variant report

Variant	rs10160758
Chromosome Location	chr11:66673079-66673080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66671241..66674201-chr11:66681070..66683415,2	MCF-7	breast:
2	chr11:66665355..66670067-chr11:66670442..66673197,5	K562	blood:
3	chr11:66671572..66673252-chr11:66674841..66677393,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173599	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10750790	0.85[ASW][hapmap];0.86[CEU][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes]
rs10791889	0.85[ASW][hapmap];0.86[CEU][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs10791895	0.83[ASN][1000 genomes]
rs10896135	0.94[CEU][hapmap]
rs10896139	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11227610	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11600959	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2077432	0.86[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2167457	0.86[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2187041	0.85[ASW][hapmap];0.81[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs2380760	0.82[EUR][1000 genomes]
rs3741194	1.00[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs4008953	0.88[EUR][1000 genomes]
rs4930390	0.85[ASW][hapmap];0.86[CEU][hapmap];0.94[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs6591222	0.82[CEU][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap]
rs7103627	0.81[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7119426	0.93[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7120256	0.93[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7122539	0.88[TSI][hapmap]
rs7570	0.90[CEU][hapmap]
rs7930203	0.85[ASW][hapmap];0.86[CEU][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7948839	0.86[CEU][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs9971487	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv897794	chr11:66579572-66744119	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv428574	chr11:66619002-66804133	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv832194	chr11:66634462-66805980	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
5	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10160758	C11orf80	cis	cerebellum	SCAN
rs10160758	B3GNT1	cis	parietal	SCAN
rs10160758	RARRES3	cis	parietal	SCAN
rs10160758	LRFN4	Cis_1M	lymphoblastoid	RTeQTL
rs10160758	CST6	cis	parietal	SCAN
rs10160758	CTSF	cis	multi-tissue	Pritchard
rs10160758	VEGFB	cis	cerebellum	SCAN
rs10160758	LRFN4	cis	multi-tissue	Pritchard
rs10160758	EHBP1L1	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66651200-66673200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:66651400-66678400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr11:66654600-66673800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:66660200-66673600	Weak transcription	HSMMtube	muscle
5	chr11:66660600-66673600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:66662200-66673600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:66664200-66673800	Weak transcription	Right Ventricle	heart
8	chr11:66665800-66673400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:66666400-66673400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr11:66667200-66673600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr11:66670000-66674000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:66670000-66675200	Weak transcription	Fetal Intestine Large	intestine
13	chr11:66670600-66673800	Weak transcription	Ovary	ovary
14	chr11:66670600-66675200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:66670800-66673200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:66670800-66673600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr11:66670800-66673600	Enhancers	Adipose Nuclei	Adipose
18	chr11:66671200-66677000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr11:66671400-66673400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:66671400-66674000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr11:66671400-66674400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr11:66671400-66674600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:66671400-66674600	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr11:66671400-66674800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr11:66671400-66675000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:66671600-66673600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:66671600-66673800	Flanking Active TSS	HepG2	liver
28	chr11:66671600-66674200	Flanking Active TSS	NHEK	skin
29	chr11:66671600-66674400	Enhancers	NH-A	brain
30	chr11:66671600-66674600	Enhancers	H1 Cell Line	embryonic stem cell
31	chr11:66671600-66674600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:66671600-66674800	Enhancers	Esophagus	oesophagus
33	chr11:66671600-66676000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:66671800-66673200	Weak transcription	Placenta	Placenta
35	chr11:66671800-66674400	Flanking Active TSS	HMEC	breast
36	chr11:66672200-66673200	Weak transcription	Colonic Mucosa	Colon
37	chr11:66672200-66674400	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr11:66672200-66674400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:66672200-66674400	Enhancers	Brain Anterior Caudate	brain
40	chr11:66672200-66674600	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr11:66672200-66674800	Enhancers	Brain Hippocampus Middle	brain
42	chr11:66672200-66675400	Weak transcription	Fetal Intestine Small	intestine
43	chr11:66672200-66675800	Flanking Active TSS	Liver	Liver
44	chr11:66672200-66676000	Enhancers	Brain Cingulate Gyrus	brain
45	chr11:66672200-66684000	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr11:66672400-66673400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr11:66672400-66673600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr11:66672400-66673600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr11:66672400-66674200	Transcr. at gene 5' and 3'	Hela-S3	cervix
50	chr11:66672600-66673400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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