Variant report

Variant	rs667476
Chromosome Location	chr15:44173755-44173756
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:44167565..44169692-chr15:44173450..44175000,2	K562	blood:
2	chr15:44166573..44169668-chr15:44170032..44175321,4	K562	blood:
3	chr15:44163547..44166358-chr15:44171239..44175142,4	K562	blood:
4	chr15:44172231..44173857-chr15:44174225..44176217,2	K562	blood:
5	chr15:44172683..44174919-chr15:44176186..44179170,4	K562	blood:

Variant related genes	Relation type
ENSG00000227973	Chromatin interaction
ENSG00000171877	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10163054	0.90[CHB][hapmap]
rs10438303	0.95[CHB][hapmap]
rs1053492	0.88[CEU][hapmap]
rs11070408	0.95[CHB][hapmap]
rs11070410	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs11638972	0.88[CEU][hapmap]
rs11852767	0.84[ASN][1000 genomes]
rs11856795	0.94[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs12440573	0.95[CHB][hapmap]
rs12441127	0.95[CHB][hapmap]
rs12441861	0.95[CHB][hapmap]
rs12441984	0.95[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs12702	0.95[CHB][hapmap]
rs16950562	0.95[CHB][hapmap]
rs16965120	0.95[CHB][hapmap]
rs16977724	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs16977798	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs1965795	0.83[ASN][1000 genomes]
rs2277531	0.95[CHB][hapmap]
rs2467402	0.89[CHB][hapmap]
rs2788	0.95[CHB][hapmap]
rs28413704	0.83[ASN][1000 genomes]
rs28476182	0.80[ASN][1000 genomes]
rs28509275	0.95[CHB][hapmap]
rs28513374	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs28519630	0.83[ASN][1000 genomes]
rs28524541	0.82[ASN][1000 genomes]
rs28531819	0.82[ASN][1000 genomes]
rs28564774	0.82[ASN][1000 genomes]
rs28636829	0.95[CHB][hapmap]
rs28679673	0.82[ASN][1000 genomes]
rs28684672	0.95[CHB][hapmap]
rs28687459	0.82[ASN][1000 genomes]
rs28696802	0.82[ASN][1000 genomes]
rs28707214	0.82[ASN][1000 genomes]
rs28780699	0.82[ASN][1000 genomes]
rs28823973	0.87[ASN][1000 genomes]
rs28858500	0.86[ASN][1000 genomes]
rs28866846	0.84[ASN][1000 genomes]
rs2955969	0.86[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs3087657	0.91[CEU][hapmap]
rs3736180	0.95[CHB][hapmap]
rs3742982	0.95[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs3759790	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs3759791	0.90[CHB][hapmap]
rs3816792	0.90[CHB][hapmap]
rs3825783	0.95[CHB][hapmap]
rs3862142	0.95[CHB][hapmap]
rs4997480	0.95[CHB][hapmap]
rs524908	0.91[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs533143	0.91[CEU][hapmap];0.95[CHB][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56909447	0.82[ASN][1000 genomes]
rs575082	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs61390361	0.93[ASN][1000 genomes]
rs663214	0.91[CEU][hapmap]
rs68079546	0.82[ASN][1000 genomes]
rs686666	0.83[CEU][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs688009	0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs693919	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs694461	0.91[CEU][hapmap];0.95[CHB][hapmap]
rs7169322	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs7169988	0.85[CHB][hapmap]
rs7171750	0.94[CHB][hapmap]
rs7174208	0.95[CHB][hapmap]
rs7175032	0.95[CHB][hapmap]
rs7175129	0.88[CEU][hapmap];0.95[CHB][hapmap]
rs7179388	0.82[ASN][1000 genomes]
rs7183809	0.82[ASN][1000 genomes]
rs8023458	0.95[CHB][hapmap]
rs8023508	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs8032649	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs8040839	0.80[ASN][1000 genomes]
rs9944216	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs9989313	0.95[CHB][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
5	nsv1050263	chr15:44093927-44204047	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs667476	STRCP1	cis	Whole Blood	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44119600-44181800	Weak transcription	Small Intestine	intestine
2	chr15:44119600-44183200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:44121000-44177600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr15:44144800-44181000	Weak transcription	HepG2	liver
5	chr15:44146800-44181600	Weak transcription	Gastric	stomach
6	chr15:44150600-44174600	Strong transcription	Dnd41	blood
7	chr15:44151600-44181600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:44152600-44180800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:44156800-44206400	Weak transcription	Fetal Brain Male	brain
10	chr15:44158200-44174000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr15:44158600-44180800	Weak transcription	Fetal Lung	lung
12	chr15:44162200-44186000	Weak transcription	HSMM	muscle
13	chr15:44163000-44179400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:44163400-44177200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr15:44164000-44175400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr15:44164800-44176000	Weak transcription	K562	blood
17	chr15:44165200-44174400	Strong transcription	Fetal Stomach	stomach
18	chr15:44165800-44177200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:44166000-44184600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:44166400-44186600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr15:44166600-44182600	Weak transcription	HUVEC	blood vessel
22	chr15:44166600-44183800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr15:44166800-44193800	Weak transcription	Spleen	Spleen
24	chr15:44166800-44196200	Weak transcription	Osteobl	bone
25	chr15:44167400-44175800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:44168000-44180200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:44168200-44176600	Strong transcription	Hela-S3	cervix
28	chr15:44168400-44174600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr15:44168800-44174000	Strong transcription	NH-A	brain
30	chr15:44169000-44174000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:44169000-44181000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr15:44169400-44174000	Enhancers	Fetal Intestine Large	intestine
33	chr15:44169800-44175200	Weak transcription	Primary T cells from cord blood	blood
34	chr15:44170200-44173800	Strong transcription	GM12878-XiMat	blood
35	chr15:44170200-44175200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:44170600-44188800	Weak transcription	NHDF-Ad	bronchial
37	chr15:44170800-44174200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:44170800-44180000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr15:44171000-44175400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:44171400-44174000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:44171600-44174400	Enhancers	Brain Substantia Nigra	brain
42	chr15:44171600-44177000	Strong transcription	Fetal Brain Female	brain
43	chr15:44171600-44181400	Strong transcription	Brain Germinal Matrix	brain
44	chr15:44172000-44173800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr15:44172000-44174000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr15:44172000-44174000	Genic enhancers	Brain Inferior Temporal Lobe	brain
47	chr15:44172200-44173800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:44172200-44174000	Enhancers	Left Ventricle	heart
49	chr15:44172200-44174000	Enhancers	Right Atrium	heart
50	chr15:44172200-44175800	Weak transcription	NHEK	skin

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