Variant report

Variant	rs61897000
Chromosome Location	chr11:74442290-74442291
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	TCF7L2	chr11:74442256-74442594	PANC-1	pancreas:	n/a	n/a
2	SUZ12	chr11:74441663-74442546	H1-hESC	embryonic stem cell:	n/a	n/a
3	GABPA	chr11:74442109-74442637	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74440853..74443969-chr11:74454724..74458008,3	K562	blood:
2	chr11:74441741..74443246-chr11:74464573..74467415,2	K562	blood:

Variant related genes	Relation type
CHRDL2	TF binding region
ENSG00000264095	Chromatin interaction
ENSG00000227615	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10899041	0.99[ASN][1000 genomes]
rs10899042	0.89[ASN][1000 genomes]
rs11236233	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11236234	0.93[ASN][1000 genomes]
rs11236236	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12223076	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12223417	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12417156	0.90[ASN][1000 genomes]
rs12419197	0.83[ASN][1000 genomes]
rs12419371	0.88[ASN][1000 genomes]
rs12576444	0.90[ASN][1000 genomes]
rs1433771	0.90[ASN][1000 genomes]
rs4944943	0.93[ASN][1000 genomes]
rs4944944	0.94[ASN][1000 genomes]
rs4944947	0.86[ASN][1000 genomes]
rs55837439	0.90[ASN][1000 genomes]
rs56187629	0.90[ASN][1000 genomes]
rs6592594	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs968305	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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs61897000	XRRA1	cis	Artery Tibial	GTEx
rs61897000	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs61897000	RP11-147I3.1	cis	Esophagus Muscularis	GTEx
rs61897000	XRRA1	cis	Esophagus Mucosa	GTEx
rs61897000	RP11-147I3.1	cis	Thyroid	GTEx
rs61897000	XRRA1	cis	lung	GTEx
rs61897000	XRRA1	cis	Heart Left Ventricle	GTEx
rs61897000	XRRA1	cis	Esophagus Muscularis	GTEx
rs61897000	XRRA1	cis	Nerve Tibial	GTEx
rs61897000	XRRA1	cis	Thyroid	GTEx
rs61897000	XRRA1	cis	Whole Blood	GTEx
rs61897000	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs61897000	XRRA1	cis	Artery Aorta	GTEx
rs61897000	XRRA1	cis	Adipose Subcutaneous	GTEx
rs61897000	XRRA1	cis	Stomach	GTEx
rs61897000	XRRA1	cis	Muscle Skeletal	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74441200-74443000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
2	chr11:74441200-74443200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr11:74441400-74443000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr11:74441600-74442400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:74441600-74442400	Bivalent Enhancer	Esophagus	oesophagus
6	chr11:74441600-74442600	Bivalent/Poised TSS	Psoas Muscle	Psoas
7	chr11:74441600-74442800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr11:74441600-74442800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:74441600-74443000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr11:74441600-74443000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr11:74441600-74443200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr11:74441800-74442400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:74441800-74442400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr11:74441800-74442600	Bivalent/Poised TSS	Left Ventricle	heart
15	chr11:74441800-74442600	Bivalent Enhancer	HMEC	breast
16	chr11:74441800-74443000	Bivalent Enhancer	Liver	Liver
17	chr11:74441800-74443000	Bivalent Enhancer	Fetal Heart	heart
18	chr11:74441800-74443000	Enhancers	Pancreas	Pancrea
19	chr11:74442000-74442400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
20	chr11:74442000-74442400	Bivalent Enhancer	Colonic Mucosa	Colon
21	chr11:74442000-74442400	Weak transcription	Gastric	stomach
22	chr11:74442000-74442400	Bivalent Enhancer	HepG2	liver
23	chr11:74442000-74442400	Bivalent Enhancer	NH-A	brain
24	chr11:74442000-74442600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr11:74442000-74442600	Bivalent Enhancer	Adipose Nuclei	Adipose
26	chr11:74442000-74442600	Bivalent Enhancer	Fetal Intestine Large	intestine
27	chr11:74442000-74442800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr11:74442000-74442800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr11:74442000-74442800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr11:74442000-74442800	Active TSS	Brain Anterior Caudate	brain
31	chr11:74442000-74443000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
32	chr11:74442000-74443000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:74442000-74443000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:74442000-74443000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:74442000-74443000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:74442000-74443000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
37	chr11:74442000-74443000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
38	chr11:74442000-74443000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
39	chr11:74442000-74443000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
40	chr11:74442000-74443000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:74442000-74443000	Active TSS	Brain Angular Gyrus	brain
42	chr11:74442000-74443000	Bivalent/Poised TSS	Brain Substantia Nigra	brain
43	chr11:74442000-74443000	Bivalent Enhancer	Placenta	Placenta
44	chr11:74442000-74443000	Active TSS	Rectal Smooth Muscle	rectum
45	chr11:74442000-74443000	Enhancers	Spleen	Spleen
46	chr11:74442000-74443000	Bivalent Enhancer	HUVEC	blood vessel
47	chr11:74442000-74443000	Bivalent/Poised TSS	Osteobl	bone
48	chr11:74442000-74443200	Bivalent Enhancer	Fetal Brain Male	brain
49	chr11:74442000-74443400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
50	chr11:74442200-74442400	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links