Variant report

Variant	rs550174
Chromosome Location	chr1:120263643-120263644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120217105..120219498-chr1:120262347..120264026,2	MCF-7	breast:
2	chr1:120262686..120264367-chr1:120265384..120267918,2	MCF-7	breast:
3	chr1:120258475..120260260-chr1:120263404..120265007,2	K562	blood:
4	chr1:120255317..120256884-chr1:120262274..120265030,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10923887	0.85[EUR][1000 genomes]
rs380155	0.80[MEX][hapmap]
rs481357	0.90[JPT][hapmap]
rs541763	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs573763	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs586650	1.00[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap];0.84[YRI][hapmap];0.94[ASN][1000 genomes]
rs598100	0.95[JPT][hapmap]
rs620741	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs636101	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs646124	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs663807	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs667770	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839613	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs839615	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs839616	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs550174	CD2	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120256000-120263800	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr1:120256200-120266600	Weak transcription	Primary B cells from cord blood	blood
3	chr1:120256200-120267400	Weak transcription	Lung	lung
4	chr1:120256200-120271800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr1:120256400-120271800	Weak transcription	Gastric	stomach
6	chr1:120256400-120276800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:120256400-120284400	Weak transcription	GM12878-XiMat	blood
8	chr1:120256600-120275600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr1:120256800-120263800	Weak transcription	HUVEC	blood vessel
10	chr1:120256800-120266000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:120257000-120263800	Weak transcription	Aorta	Aorta
12	chr1:120257000-120266000	Weak transcription	HSMMtube	muscle
13	chr1:120257000-120271800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr1:120257000-120277400	Weak transcription	Fetal Heart	heart
15	chr1:120257000-120278400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:120257000-120278600	Weak transcription	HSMM	muscle
17	chr1:120257000-120282400	Weak transcription	A549	lung
18	chr1:120257200-120287000	Weak transcription	NH-A	brain
19	chr1:120257600-120263800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:120257600-120264400	Weak transcription	Placenta	Placenta
21	chr1:120257600-120268000	Weak transcription	Fetal Brain Male	brain
22	chr1:120258600-120263800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:120258600-120267200	Weak transcription	Fetal Brain Female	brain
24	chr1:120258600-120289200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:120258800-120263800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:120258800-120266000	Weak transcription	Esophagus	oesophagus
27	chr1:120258800-120269400	Weak transcription	Spleen	Spleen
28	chr1:120258800-120275000	Weak transcription	Right Atrium	heart
29	chr1:120259000-120265800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:120259200-120263800	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:120259200-120263800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:120259200-120264000	Weak transcription	Brain Germinal Matrix	brain
33	chr1:120259200-120264000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:120259200-120264000	Weak transcription	K562	blood
35	chr1:120259200-120265600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:120259200-120277800	Weak transcription	Right Ventricle	heart
37	chr1:120260400-120287600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:120260600-120266000	Enhancers	Pancreas	Pancrea
39	chr1:120261000-120265800	Weak transcription	Brain Angular Gyrus	brain
40	chr1:120261000-120274200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:120261000-120287200	Strong transcription	Hela-S3	cervix
42	chr1:120261200-120263800	Weak transcription	Brain Anterior Caudate	brain
43	chr1:120261200-120264200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:120261200-120269400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:120261400-120268800	Weak transcription	Small Intestine	intestine
46	chr1:120261400-120274800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:120261600-120273600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:120261600-120288200	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:120261800-120267800	Genic enhancers	HepG2	liver
50	chr1:120261800-120281600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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