Variant report

Variant	rs11079747
Chromosome Location	chr17:45078850-45078851
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45078439..45078999-chr4:28740495..28741046,2	MCF-7	breast:
2	chr17:45019636..45020289-chr17:45077991..45079169,4	MCF-7	breast:
3	chr17:37391666..37392167-chr17:45078559..45079144,2	MCF-7	breast:
4	chr17:45019970..45020552-chr17:45078269..45079135,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11079750	0.94[ASW][hapmap];0.81[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap]
rs11653589	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11653838	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11658863	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11871052	0.82[AFR][1000 genomes]
rs12938690	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12949446	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12952596	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1476498	0.83[JPT][hapmap]
rs1634265	0.83[JPT][hapmap]
rs1713493	0.83[JPT][hapmap]
rs2316758	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36056466	0.81[EUR][1000 genomes]
rs3851792	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3851795	0.95[ASN][1000 genomes]
rs3851796	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3851798	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3851799	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4074249	0.80[CEU][hapmap];0.90[LWK][hapmap];0.92[MKK][hapmap];0.87[YRI][hapmap]
rs4572469	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4968300	0.83[AFR][1000 genomes]
rs4968304	0.80[CEU][hapmap];0.92[YRI][hapmap]
rs62073762	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7216950	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs8064936	0.81[EUR][1000 genomes]
rs8068715	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8071243	0.83[JPT][hapmap]
rs858677	0.83[JPT][hapmap]
rs9747243	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
7	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
9	nsv833467	chr17:45063935-45252624	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11079747	LRRC46	cis	lymphoblastoid	seeQTL
rs11079747	IFI35	cis	parietal	SCAN
rs11079747	C17orf53	cis	parietal	SCAN
rs11079747	LRRC46	cis	parietal	SCAN
rs11079747	STAT5B	cis	parietal	SCAN
rs11079747	GOSR2	Cis_1M	lymphoblastoid	RTeQTL
rs11079747	MRPL10	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45057200-45086800	Weak transcription	Right Atrium	heart
2	chr17:45057200-45100000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr17:45057800-45082400	Weak transcription	Brain Angular Gyrus	brain
4	chr17:45060200-45080800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr17:45061400-45086600	Weak transcription	Fetal Stomach	stomach
6	chr17:45061800-45087600	Weak transcription	Spleen	Spleen
7	chr17:45062200-45113200	Weak transcription	Ovary	ovary
8	chr17:45064200-45083000	Weak transcription	Brain Germinal Matrix	brain
9	chr17:45071200-45082200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:45073000-45082400	Weak transcription	Brain Substantia Nigra	brain
11	chr17:45074000-45081800	Weak transcription	HUVEC	blood vessel
12	chr17:45075200-45130200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr17:45076400-45087000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:45078000-45080000	Enhancers	Primary B cells from cord blood	blood
15	chr17:45078200-45079200	Enhancers	Primary T cells fromperipheralblood	blood
16	chr17:45078200-45079400	Enhancers	Primary B cells from peripheral blood	blood
17	chr17:45078400-45079000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr17:45078400-45079000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr17:45078400-45079000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr17:45078400-45079000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr17:45078400-45079000	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr17:45078400-45079000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr17:45078400-45079000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:45078400-45079000	Active TSS	Adipose Nuclei	Adipose
25	chr17:45078400-45079000	Enhancers	Brain Hippocampus Middle	brain
26	chr17:45078400-45079200	Enhancers	GM12878-XiMat	blood
27	chr17:45078400-45079400	Enhancers	Dnd41	blood
28	chr17:45078400-45079400	Flanking Active TSS	HepG2	liver
29	chr17:45078600-45079000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr17:45078600-45081600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr17:45078600-45082800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr17:45078600-45087000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr17:45078800-45079000	Enhancers	Muscle Satellite Cultured Cells	--
34	chr17:45078800-45079200	Enhancers	Primary hematopoietic stem cells	blood
35	chr17:45078800-45079400	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr17:45078800-45079600	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr17:45078800-45079600	Enhancers	Monocytes-CD14+_RO01746	blood

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