Variant report

Variant	rs55837439
Chromosome Location	chr11:74433193-74433194
allele	A/G
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	MAZ	chr11:74431451-74433242	IMR90	lung:	n/a	chr11:74432290-74432300

No.	Distal block	Cell Line	Cell type
1	chr11:74426377..74428820-chr11:74432768..74435439,2	K562	blood:
2	chr11:74429748..74431505-chr11:74431883..74434442,2	K562	blood:
3	chr11:74431447..74433906-chr11:74434209..74436867,2	MCF-7	breast:
4	chr11:74429451..74431505-chr11:74431883..74434860,3	K562	blood:
5	chr11:74428350..74430634-chr11:74431108..74433970,2	MCF-7	breast:

Variant related genes	Relation type
MIR4696	TF binding region
CHRDL2	TF binding region
ENSG00000265902	Chromatin interaction
ENSG00000212277	Chromatin interaction
ENSG00000054938	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10899041	0.91[ASN][1000 genomes]
rs10899042	0.81[ASN][1000 genomes]
rs11236233	0.98[ASN][1000 genomes]
rs11236234	0.94[ASN][1000 genomes]
rs11236236	0.90[ASN][1000 genomes]
rs12417156	0.97[ASN][1000 genomes]
rs12419371	0.82[ASN][1000 genomes]
rs12576444	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1433771	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4944943	0.94[ASN][1000 genomes]
rs4944944	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56187629	0.91[ASN][1000 genomes]
rs61897000	0.90[ASN][1000 genomes]
rs968305	0.94[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs55837439	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs55837439	XRRA1	cis	Whole Blood	GTEx
rs55837439	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs55837439	XRRA1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:34 , 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	chr11:74429200-74434200	Enhancers	Colon Smooth Muscle	Colon
4	chr11:74429200-74434800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:74429600-74434400	Enhancers	Brain Anterior Caudate	brain
6	chr11:74430400-74433200	Enhancers	Fetal Muscle Leg	muscle
7	chr11:74430600-74433200	Enhancers	Brain Cingulate Gyrus	brain
8	chr11:74430600-74434400	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr11:74430600-74434800	Enhancers	Brain Angular Gyrus	brain
10	chr11:74431400-74433400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr11:74432000-74434000	Enhancers	Lung	lung
12	chr11:74432200-74434600	Enhancers	Brain Hippocampus Middle	brain
13	chr11:74432400-74434200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:74432600-74433200	Enhancers	Rectal Mucosa Donor 29	rectum
15	chr11:74432600-74433200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr11:74432600-74433600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr11:74432600-74435600	Weak transcription	Right Ventricle	heart
18	chr11:74432600-74437000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr11:74432600-74437000	Weak transcription	Stomach Mucosa	stomach
20	chr11:74432600-74437400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr11:74432600-74437600	Weak transcription	Brain Germinal Matrix	brain
22	chr11:74432800-74433200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr11:74432800-74433200	Enhancers	Stomach Smooth Muscle	stomach
24	chr11:74432800-74434400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:74432800-74436400	Weak transcription	Fetal Heart	heart
26	chr11:74432800-74436600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:74432800-74436800	Weak transcription	Placenta	Placenta
28	chr11:74432800-74436800	Weak transcription	Left Ventricle	heart
29	chr11:74432800-74437000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr11:74432800-74437200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr11:74432800-74437400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:74432800-74442000	Weak transcription	Right Atrium	heart
33	chr11:74432800-74442000	Weak transcription	Spleen	Spleen
34	chr11:74433000-74433400	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links