Variant report

Variant	rs11708227
Chromosome Location	chr3:53748033-53748034
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	chr3:53747075..53750039-chr3:53753263..53755603,3	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10510765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10510766	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11705918	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706303	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11708934	0.84[EUR][1000 genomes]
rs11709505	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075639	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076366	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076915	1.00[CHB][hapmap]
rs13082692	0.81[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17053338	1.00[CHB][hapmap]
rs17053417	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs17053532	1.00[ASN][1000 genomes]
rs17641133	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2029331	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs2118421	1.00[ASN][1000 genomes]
rs2125876	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232333	1.00[ASN][1000 genomes]
rs2359204	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2612012	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs2633726	1.00[ASN][1000 genomes]
rs28675949	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35377175	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35414202	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35657034	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4453827	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45560831	1.00[ASN][1000 genomes]
rs45616236	1.00[ASN][1000 genomes]
rs4687586	1.00[CHB][hapmap]
rs4687736	0.83[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes]
rs55974100	1.00[ASN][1000 genomes]
rs56052250	1.00[ASN][1000 genomes]
rs6445606	1.00[CHB][hapmap]
rs6800641	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs723540	0.86[EUR][1000 genomes]
rs73092085	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628839	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs893363	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1007655	chr3:53742148-53767689	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1002452	chr3:53742148-53802811	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1000280	chr3:53742736-53770588	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11708227	HEMK1	cis	cerebellum	SCAN
rs11708227	CCDC66	cis	parietal	SCAN
rs11708227	SEMA3G	cis	parietal	SCAN
rs11708227	IL17RB	cis	cerebellum	SCAN
rs11708227	FAM116A	cis	cerebellum	SCAN
rs11708227	RBM6	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53740200-53764400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:53741200-53751400	Weak transcription	Fetal Brain Female	brain
3	chr3:53742600-53778000	Weak transcription	Pancreas	Pancrea
4	chr3:53744200-53753800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:53744200-53764600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:53744400-53748200	Weak transcription	Fetal Heart	heart
7	chr3:53744400-53749400	Weak transcription	Right Ventricle	heart
8	chr3:53744400-53749800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:53744400-53756600	Weak transcription	Lung	lung
10	chr3:53744400-53758600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:53744400-53763800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:53744600-53749600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:53744600-53755000	Weak transcription	Brain Anterior Caudate	brain
14	chr3:53744600-53755000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:53744600-53756400	Weak transcription	Liver	Liver
16	chr3:53744600-53761200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:53745000-53753800	Strong transcription	Fetal Intestine Small	intestine
18	chr3:53745200-53762800	Strong transcription	Fetal Intestine Large	intestine
19	chr3:53745400-53748400	Enhancers	Left Ventricle	heart
20	chr3:53745600-53750200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:53746400-53749200	Weak transcription	Fetal Lung	lung
22	chr3:53746800-53749200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr3:53747200-53748200	Weak transcription	Right Atrium	heart
24	chr3:53747400-53751000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr3:53747800-53748200	Weak transcription	Spleen	Spleen
26	chr3:53747800-53749000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:53748000-53748400	Weak transcription	Fetal Brain Male	brain

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