Variant report

Variant	rs12576444
Chromosome Location	chr11:74435861-74435862
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:74423812..74427118-chr11:74435332..74438905,3	MCF-7	breast:
2	chr11:74434860..74436496-chr11:74441667..74443520,2	K562	blood:
3	chr11:74423556..74425129-chr11:74434976..74437212,2	K562	blood:
4	chr11:74429602..74433015-chr11:74434842..74437156,4	K562	blood:
5	chr11:74431447..74433906-chr11:74434209..74436867,2	MCF-7	breast:
6	chr11:74431341..74433015-chr11:74435412..74437156,2	K562	blood:
7	chr11:74431181..74434029-chr11:74434505..74437291,2	MCF-7	breast:
8	chr11:74433572..74436146-chr11:74437408..74439019,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000054938	Chromatin interaction
ENSG00000265902	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 18 )

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

rs_ID	r²[population]
rs10899041	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899042	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11236233	0.99[ASN][1000 genomes]
rs11236234	0.94[ASN][1000 genomes]
rs11236236	0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs12417156	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12419197	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12419371	0.81[ASN][1000 genomes]
rs1433771	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17133461	0.84[CHD][hapmap]
rs4483614	0.84[CHD][hapmap]
rs4944943	0.93[ASN][1000 genomes]
rs4944944	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4944947	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4944950	0.84[CHD][hapmap]
rs55837439	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs56187629	0.90[ASN][1000 genomes]
rs61897000	0.90[ASN][1000 genomes]
rs7103136	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs7948433	0.84[CHD][hapmap]
rs968305	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.93[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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs12576444	XRRA1	cis	Stomach	GTEx
rs12576444	XRRA1	cis	Adipose Subcutaneous	GTEx
rs12576444	XRRA1	cis	cerebellum	SCAN
rs12576444	XRRA1	cis	Artery Tibial	GTEx
rs12576444	XRRA1	cis	Thyroid	GTEx
rs12576444	XRRA1	cis	multi-tissue	Pritchard
rs12576444	XRRA1	cis	parietal	SCAN
rs12576444	XRRA1	cis	Esophagus Mucosa	GTEx
rs12576444	RP11-147I3.1	cis	Thyroid	GTEx
rs12576444	NEU3	cis	cerebellum	SCAN
rs12576444	XRRA1	cis	Esophagus Muscularis	GTEx
rs12576444	XRRA1	cis	Muscle Skeletal	GTEx
rs12576444	XRRA1	cis	Nerve Tibial	GTEx
rs12576444	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs12576444	XRRA1	cis	lymphoblastoid	seeQTL
rs12576444	KRTAP5-11	cis	parietal	SCAN
rs12576444	XRRA1	cis	Whole Blood	GTEx
rs12576444	PAAF1	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74432600-74437000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr11:74432600-74437000	Weak transcription	Stomach Mucosa	stomach
3	chr11:74432600-74437400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr11:74432600-74437600	Weak transcription	Brain Germinal Matrix	brain
5	chr11:74432800-74436400	Weak transcription	Fetal Heart	heart
6	chr11:74432800-74436600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr11:74432800-74436800	Weak transcription	Placenta	Placenta
8	chr11:74432800-74436800	Weak transcription	Left Ventricle	heart
9	chr11:74432800-74437000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr11:74432800-74437200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr11:74432800-74437400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:74432800-74442000	Weak transcription	Right Atrium	heart
13	chr11:74432800-74442000	Weak transcription	Spleen	Spleen
14	chr11:74433200-74436600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:74433400-74439000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:74434000-74437000	Weak transcription	Lung	lung
17	chr11:74434200-74436400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:74434200-74438400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr11:74434400-74437200	Weak transcription	Brain Anterior Caudate	brain
20	chr11:74434400-74437400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr11:74434400-74437600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr11:74434600-74436400	Weak transcription	Fetal Stomach	stomach
23	chr11:74434600-74437200	Weak transcription	Brain Hippocampus Middle	brain
24	chr11:74434800-74437000	Weak transcription	Brain Substantia Nigra	brain
25	chr11:74434800-74442000	Weak transcription	Brain Angular Gyrus	brain
26	chr11:74435800-74436400	Weak transcription	Right Ventricle	heart
27	chr11:74435800-74438000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr11:74435800-74438200	Enhancers	Colon Smooth Muscle	Colon
29	chr11:74435800-74438200	Bivalent Enhancer	Fetal Muscle Leg	muscle

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