Variant report

Variant	rs2337360
Chromosome Location	chr1:151514603-151514604
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr1:151511796-151515943	IMR90	lung:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151481429..151491154-chr1:151502501..151517487,49	MCF-7	breast:
2	chr1:151421812..151434588-chr1:151506621..151515599,30	MCF-7	breast:
3	chr1:151511929..151514676-chr5:16935884..16938127,2	MCF-7	breast:
4	chr1:151510867..151515069-chr1:151533037..151539348,7	MCF-7	breast:
5	chr1:151510723..151515515-chr1:151802413..151805096,5	MCF-7	breast:
6	chr1:151512668..151514795-chr1:151529335..151532212,2	K562	blood:
7	chr1:151514211..151516187-chr1:151541825..151543936,2	MCF-7	breast:
8	chr1:151514171..151515908-chr1:151540816..151544051,3	MCF-7	breast:
9	chr1:151510726..151515686-chr1:151583230..151586215,6	MCF-7	breast:
10	chr1:151370811..151373589-chr1:151512732..151514796,2	K562	blood:
11	chr1:151372028..151374418-chr1:151511841..151514665,2	MCF-7	breast:
12	chr1:151477348..151494376-chr1:151504804..151515249,50	MCF-7	breast:
13	chr1:151510534..151515854-chr1:151533093..151539013,11	MCF-7	breast:
14	chr1:151513420..151515401-chr1:151965991..151967960,2	MCF-7	breast:
15	chr1:151513355..151515892-chr1:151812476..151814438,2	MCF-7	breast:
16	chr1:151512582..151515033-chr8:145580545..145582400,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR554	TF binding region
ENSG00000250734	Chromatin interaction
ENSG00000145555	Chromatin interaction
ENSG00000234614	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000201134	Chromatin interaction
ENSG00000143442	Chromatin interaction
ENSG00000143365	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000229021	Chromatin interaction
ENSG00000223861	Chromatin interaction
ENSG00000143367	Chromatin interaction
ENSG00000159377	Chromatin interaction
ENSG00000182325	Chromatin interaction
ENSG00000225556	Chromatin interaction
ENSG00000185803	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10158855	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204842	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204845	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204846	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204847	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12034149	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12117155	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12753658	0.96[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1891593	0.96[CEU][hapmap];0.82[CHD][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs34589182	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35436273	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3828055	0.86[CHB][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4970956	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4970958	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56096667	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56188938	0.84[EUR][1000 genomes]
rs6669998	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7521397	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7526319	0.87[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7549296	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs868138	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
2	nsv997511	chr1:151491765-151595902	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2337360	OTUD7B	cis	cerebellum	SCAN
rs2337360	CTSS	cis	cerebellum	SCAN
rs2337360	ZNF687	cis	parietal	SCAN
rs2337360	LINGO4	cis	cerebellum	SCAN
rs2337360	S100A8	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151512000-151514800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:151512400-151515600	Active TSS	Esophagus	oesophagus
3	chr1:151512600-151515000	Active TSS	Fetal Intestine Small	intestine
4	chr1:151512600-151515000	Active TSS	A549	lung
5	chr1:151513000-151515000	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr1:151513400-151515800	Flanking Active TSS	Hela-S3	cervix
7	chr1:151513600-151515600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
8	chr1:151513800-151515200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:151513800-151515400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:151513800-151515600	Flanking Active TSS	Osteobl	bone
11	chr1:151513800-151519400	Weak transcription	Left Ventricle	heart
12	chr1:151514000-151514800	Enhancers	Liver	Liver
13	chr1:151514000-151515200	Weak transcription	Gastric	stomach
14	chr1:151514000-151515600	Enhancers	Aorta	Aorta
15	chr1:151514000-151515600	Enhancers	Fetal Muscle Leg	muscle
16	chr1:151514000-151515800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:151514000-151515800	Flanking Active TSS	HSMM	muscle
18	chr1:151514000-151516200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:151514000-151519400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:151514000-151519400	Weak transcription	HUVEC	blood vessel
21	chr1:151514200-151515200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:151514200-151515200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:151514200-151515400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:151514200-151515400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:151514200-151515600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:151514200-151515600	Enhancers	Brain Germinal Matrix	brain
27	chr1:151514200-151515600	Transcr. at gene 5' and 3'	NHEK	skin
28	chr1:151514200-151515800	Enhancers	Colon Smooth Muscle	Colon
29	chr1:151514200-151516200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:151514200-151516200	Flanking Active TSS	HSMMtube	muscle
31	chr1:151514200-151517800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:151514200-151519400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:151514200-151519400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:151514200-151519400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:151514200-151519600	Weak transcription	Fetal Heart	heart
36	chr1:151514200-151519600	Weak transcription	Ovary	ovary
37	chr1:151514400-151514800	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr1:151514400-151514800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:151514400-151514800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:151514400-151514800	Flanking Active TSS	Fetal Intestine Large	intestine
41	chr1:151514400-151514800	Weak transcription	Fetal Kidney	kidney
42	chr1:151514400-151515000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:151514400-151515200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:151514400-151515200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:151514400-151515400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:151514400-151515400	Active TSS	Colonic Mucosa	Colon
47	chr1:151514400-151515400	Enhancers	Stomach Mucosa	stomach
48	chr1:151514400-151515600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:151514400-151515600	Enhancers	HepG2	liver
50	chr1:151514400-151516200	Enhancers	Adipose Nuclei	Adipose

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