Variant report

Variant	rs2235377
Chromosome Location	chr1:209975392-209975393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209974237..209976657-chr1:209978058..209981003,3	K562	blood:
2	chr1:209974477..209976962-chr1:209977891..209979469,2	MCF-7	breast:
3	chr1:209958606..209961246-chr1:209973550..209976119,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232222	Chromatin interaction
ENSG00000117595	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10489343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779514	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10779515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10863789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1109430	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11119345	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11119346	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119360	1.00[AFR][1000 genomes]
rs11585733	1.00[AFR][1000 genomes]
rs11589335	1.00[AFR][1000 genomes]
rs12058100	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12062600	1.00[AFR][1000 genomes]
rs12063989	1.00[AFR][1000 genomes]
rs12064085	1.00[AFR][1000 genomes]
rs12064211	1.00[AFR][1000 genomes]
rs12064398	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12066340	1.00[AFR][1000 genomes]
rs12069187	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12075674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12080691	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12081405	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12083685	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.93[EUR][1000 genomes]
rs12405750	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12561766	1.00[AFR][1000 genomes]
rs12563527	1.00[AFR][1000 genomes]
rs12566152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13306422	1.00[AFR][1000 genomes]
rs17015217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17015268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1856161	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1883332	1.00[AFR][1000 genomes]
rs2038053	1.00[AFR][1000 genomes]
rs2069068	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076149	1.00[AFR][1000 genomes]
rs2076151	1.00[AFR][1000 genomes]
rs2142860	1.00[AFR][1000 genomes]
rs2235370	0.85[AMR][1000 genomes]
rs2235371	1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272866	1.00[AFR][1000 genomes]
rs2282740	1.00[AFR][1000 genomes]
rs3753517	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41274836	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4140636	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.80[EUR][1000 genomes]
rs4329516	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4844491	1.00[AFR][1000 genomes]
rs4844494	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4844496	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4844893	1.00[AFR][1000 genomes]
rs4844894	1.00[AFR][1000 genomes]
rs4844908	1.00[AFR][1000 genomes]
rs57283682	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2235377	SNORD117	trans	lymphoblastoid	seeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209957800-209978600	Weak transcription	Spleen	Spleen
2	chr1:209958400-209978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:209958600-209978800	Weak transcription	Right Ventricle	heart
4	chr1:209962200-209977800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:209963000-209978800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:209964200-209976000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:209964200-209977800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:209964200-209978000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:209964400-209978200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:209965200-209975400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:209966000-209976200	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr1:209966000-209978000	Weak transcription	Colonic Mucosa	Colon
13	chr1:209966000-209978400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:209969000-209976400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:209969000-209978600	Weak transcription	Lung	lung
16	chr1:209970000-209975400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr1:209971000-209976000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:209972000-209978400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:209972000-209978600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:209973200-209975400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:209973200-209976000	Weak transcription	Esophagus	oesophagus
22	chr1:209973200-209976200	Weak transcription	Gastric	stomach
23	chr1:209974000-209975800	Enhancers	Aorta	Aorta
24	chr1:209974000-209976400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
25	chr1:209974200-209975600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr1:209974200-209976200	Genic enhancers	Fetal Intestine Large	intestine
27	chr1:209974200-209978200	Transcr. at gene 5' and 3'	HMEC	breast
28	chr1:209974200-209978800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:209974400-209975600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:209974600-209975600	Flanking Active TSS	HUVEC	blood vessel
31	chr1:209974600-209975800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:209974600-209975800	Bivalent Enhancer	Fetal Muscle Leg	muscle
33	chr1:209974600-209976400	Genic enhancers	Fetal Intestine Small	intestine
34	chr1:209974600-209976600	Enhancers	Stomach Mucosa	stomach
35	chr1:209974600-209977000	Enhancers	Small Intestine	intestine
36	chr1:209974600-209977800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:209974600-209978000	Enhancers	Pancreas	Pancrea
38	chr1:209974600-209978200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:209974800-209975400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:209974800-209975400	Active TSS	Left Ventricle	heart
41	chr1:209974800-209975600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:209974800-209975600	Active TSS	Right Atrium	heart
43	chr1:209974800-209975600	Enhancers	HSMMtube	muscle
44	chr1:209974800-209975600	Enhancers	Osteobl	bone
45	chr1:209974800-209976800	Weak transcription	Placenta	Placenta
46	chr1:209974800-209979000	Transcr. at gene 5' and 3'	NHEK	skin
47	chr1:209975000-209975600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:209975000-209975600	Flanking Active TSS	Liver	Liver
49	chr1:209975000-209976800	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr1:209975200-209975400	Flanking Active TSS	Fetal Heart	heart

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