Variant report

Variant	rs12417156
Chromosome Location	chr11:74429987-74429988
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	chr11:74428350..74430634-chr11:74431108..74433970,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265902	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10899041	0.89[ASN][1000 genomes]
rs10899042	0.91[CHD][hapmap]
rs11236233	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11236234	0.91[ASN][1000 genomes]
rs11236236	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12223417	0.86[CEU][hapmap]
rs12419371	0.90[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12576444	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1433771	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17133461	0.84[CHD][hapmap]
rs4483614	0.84[CHD][hapmap]
rs4944943	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944944	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs4944947	0.91[CHD][hapmap]
rs4944950	0.84[CHD][hapmap]
rs55837439	0.97[ASN][1000 genomes]
rs56187629	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61897000	0.90[ASN][1000 genomes]
rs7103136	0.90[CHD][hapmap]
rs7948433	0.95[CEU][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs968305	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs12417156	XRRA1	cis	Muscle Skeletal	GTEx
rs12417156	XRRA1	cis	Esophagus Mucosa	GTEx
rs12417156	RNF169	cis	cerebellum	SCAN
rs12417156	XRRA1	cis	lymphoblastoid	seeQTL
rs12417156	MRPL48	cis	cerebellum	SCAN
rs12417156	NDUFC2	cis	parietal	SCAN
rs12417156	XRRA1	cis	Nerve Tibial	GTEx
rs12417156	XRRA1	cis	Stomach	GTEx
rs12417156	INPPL1	cis	parietal	SCAN
rs12417156	PAAF1	cis	parietal	SCAN
rs12417156	XRRA1	cis	Adipose Subcutaneous	GTEx
rs12417156	XRRA1	cis	lymphoblastoid	GTEx
rs12417156	XRRA1	cis	Whole Blood	GTEx
rs12417156	XRRA1	cis	lung	GTEx
rs12417156	XRRA1	cis	cerebellum	SCAN
rs12417156	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs12417156	XRRA1	cis	Esophagus Muscularis	GTEx
rs12417156	XRRA1	cis	multi-tissue	Pritchard
rs12417156	XRRA1	cis	parietal	SCAN
rs12417156	XRRA1	cis	Artery Tibial	GTEx
rs12417156	XRRA1	cis	Thyroid	GTEx
rs12417156	XRRA1	cis	Heart Left Ventricle	GTEx
rs12417156	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74422000-74430800	Weak transcription	Right Atrium	heart
2	chr11:74422400-74430800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:74427200-74434600	Enhancers	Fetal Stomach	stomach
4	chr11:74427800-74434200	Enhancers	Rectal Smooth Muscle	rectum
5	chr11:74428200-74432600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr11:74428600-74430800	Weak transcription	Right Ventricle	heart
7	chr11:74428600-74431400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:74428600-74431600	Enhancers	Stomach Smooth Muscle	stomach
9	chr11:74428800-74431000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:74428800-74431400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr11:74428800-74432000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:74429000-74430800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:74429000-74431200	Weak transcription	Fetal Intestine Small	intestine
14	chr11:74429000-74431600	Weak transcription	Fetal Intestine Large	intestine
15	chr11:74429200-74430600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:74429200-74430600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:74429200-74430600	Weak transcription	Fetal Lung	lung
18	chr11:74429200-74430800	Weak transcription	Brain Substantia Nigra	brain
19	chr11:74429200-74430800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr11:74429200-74431400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr11:74429200-74431400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:74429200-74431800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:74429200-74434200	Enhancers	Colon Smooth Muscle	Colon
24	chr11:74429200-74434800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:74429400-74430400	Weak transcription	Brain Hippocampus Middle	brain
26	chr11:74429400-74430600	Weak transcription	Brain Angular Gyrus	brain
27	chr11:74429600-74430800	Weak transcription	Ovary	ovary
28	chr11:74429600-74434400	Enhancers	Brain Anterior Caudate	brain
29	chr11:74429800-74430000	Enhancers	Esophagus	oesophagus
30	chr11:74429800-74430800	Weak transcription	Placenta	Placenta
31	chr11:74429800-74431800	Weak transcription	Aorta	Aorta

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