Variant report

Variant	rs4944943
Chromosome Location	chr11:74431277-74431278
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr11:74431231-74432810	IMR90	lung:	n/a	n/a

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
ENSG00000212277	TF binding region
CHRDL2	TF binding region
ENSG00000054938	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10899041	0.92[ASN][1000 genomes]
rs10899042	0.82[ASN][1000 genomes]
rs11236233	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11236234	0.94[ASN][1000 genomes]
rs11236236	0.93[ASN][1000 genomes]
rs12223076	0.80[ASN][1000 genomes]
rs12223417	0.80[ASN][1000 genomes]
rs12417156	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12419371	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12576444	0.93[ASN][1000 genomes]
rs1433771	0.94[ASN][1000 genomes]
rs4944944	0.96[ASN][1000 genomes]
rs55837439	0.94[ASN][1000 genomes]
rs56187629	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61897000	0.93[ASN][1000 genomes]
rs7948433	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs968305	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4944943	XRRA1	cis	Esophagus Muscularis	GTEx
rs4944943	XRRA1	cis	Adipose Subcutaneous	GTEx
rs4944943	XRRA1	cis	Thyroid	GTEx
rs4944943	XRRA1	cis	Muscle Skeletal	GTEx
rs4944943	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs4944943	XRRA1	cis	Whole Blood	GTEx
rs4944943	XRRA1	cis	Heart Left Ventricle	GTEx
rs4944943	XRRA1	cis	Esophagus Mucosa	GTEx
rs4944943	XRRA1	cis	Nerve Tibial	GTEx
rs4944943	XRRA1	cis	Stomach	GTEx
rs4944943	XRRA1	cis	Artery Tibial	GTEx
rs4944943	XRRA1	cis	lung	GTEx
rs4944943	XRRA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74427200-74434600	Enhancers	Fetal Stomach	stomach
2	chr11:74427800-74434200	Enhancers	Rectal Smooth Muscle	rectum
3	chr11:74428200-74432600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr11:74428600-74431400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:74428600-74431600	Enhancers	Stomach Smooth Muscle	stomach
6	chr11:74428800-74431400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:74428800-74432000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:74429000-74431600	Weak transcription	Fetal Intestine Large	intestine
9	chr11:74429200-74431400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:74429200-74431400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr11:74429200-74431800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:74429200-74434200	Enhancers	Colon Smooth Muscle	Colon
13	chr11:74429200-74434800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:74429600-74434400	Enhancers	Brain Anterior Caudate	brain
15	chr11:74429800-74431800	Weak transcription	Aorta	Aorta
16	chr11:74430000-74432400	Weak transcription	Esophagus	oesophagus
17	chr11:74430200-74432000	Enhancers	Colonic Mucosa	Colon
18	chr11:74430400-74431800	Enhancers	Brain Hippocampus Middle	brain
19	chr11:74430400-74433200	Enhancers	Fetal Muscle Leg	muscle
20	chr11:74430600-74432600	Enhancers	Brain Germinal Matrix	brain
21	chr11:74430600-74432800	Enhancers	Fetal Lung	lung
22	chr11:74430600-74433200	Enhancers	Brain Cingulate Gyrus	brain
23	chr11:74430600-74434400	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr11:74430600-74434800	Enhancers	Brain Angular Gyrus	brain
25	chr11:74430800-74431800	Enhancers	Brain Substantia Nigra	brain
26	chr11:74430800-74432000	Weak transcription	Lung	lung
27	chr11:74430800-74432400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr11:74430800-74432400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr11:74430800-74432600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr11:74430800-74432600	Enhancers	Ovary	ovary
31	chr11:74430800-74432600	Enhancers	Right Ventricle	heart
32	chr11:74430800-74432800	Enhancers	Placenta	Placenta
33	chr11:74430800-74432800	Enhancers	Left Ventricle	heart
34	chr11:74430800-74432800	Enhancers	Right Atrium	heart
35	chr11:74431000-74431600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr11:74431000-74431800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr11:74431000-74432000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr11:74431000-74432200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr11:74431000-74432400	Enhancers	Fetal Muscle Trunk	muscle
40	chr11:74431000-74432800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:74431200-74432400	Enhancers	Fetal Intestine Small	intestine
42	chr11:74431200-74432800	Enhancers	Fetal Heart	heart

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