Variant report

Variant	rs5002947
Chromosome Location	chr1:160578141-160578142
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160524454..160527285-chr1:160577181..160579481,2	K562	blood:
2	chr1:160312315..160314357-chr1:160577334..160579033,2	MCF-7	breast:
3	chr1:160577461..160579543-chr1:160581700..160584306,2	K562	blood:

Variant related genes	Relation type
ENSG00000122218	Chromatin interaction
ENSG00000162736	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1055880	0.95[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs1061217	0.83[CEU][hapmap]
rs11265442	0.84[CEU][hapmap]
rs11265452	0.91[CEU][hapmap]
rs11583402	0.95[CEU][hapmap]
rs11585738	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs11590035	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12144628	0.84[CEU][hapmap]
rs12402879	0.84[CEU][hapmap]
rs12728784	0.87[CEU][hapmap]
rs1394078	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs151607	0.83[CEU][hapmap]
rs1572382	0.84[CEU][hapmap]
rs16832283	0.91[CEU][hapmap]
rs1726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17381453	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs17385337	0.87[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs17385407	0.96[CEU][hapmap];0.82[TSI][hapmap]
rs17385878	0.90[EUR][1000 genomes]
rs1809963	0.91[CEU][hapmap]
rs1998651	0.84[CEU][hapmap]
rs2025516	0.81[CEU][hapmap]
rs2083128	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs2099604	0.91[CEU][hapmap]
rs2753260	0.83[CEU][hapmap]
rs3733264	0.96[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap]
rs3733265	0.96[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap]
rs3733266	0.96[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs3755898	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3766384	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3766385	0.96[CEU][hapmap]
rs3766387	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3766388	0.91[CEU][hapmap]
rs3766389	0.96[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs3816146	0.88[CEU][hapmap]
rs56040770	0.82[EUR][1000 genomes]
rs61801562	0.88[EUR][1000 genomes]
rs61801564	0.81[EUR][1000 genomes]
rs61801565	0.82[EUR][1000 genomes]
rs61801567	0.84[EUR][1000 genomes]
rs6662093	0.85[EUR][1000 genomes]
rs6668760	0.84[CEU][hapmap]
rs6670721	1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs6687641	0.92[CEU][hapmap];0.91[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs6692382	0.84[CEU][hapmap]
rs7547054	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7550771	0.83[CEU][hapmap];0.80[TSI][hapmap]
rs912582	0.96[CEU][hapmap]
rs977019	0.84[CEU][hapmap]

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	esv1829614	chr1:160465291-160595000	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv872491	chr1:160470258-160580549	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831703	chr1:160496124-160643024	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs5002947	NHLH1	cis	cerebellum	SCAN
rs5002947	CD84	Cis_1M	lymphoblastoid	RTeQTL
rs5002947	CD84	cis	lymphoblastoid	seeQTL
rs5002947	ATF6	cis	parietal	SCAN
rs5002947	VANGL2	cis	cerebellum	SCAN
rs5002947	HCN3	cis	cerebellum	SCAN
rs5002947	SLAMF6	cis	lymphoblastoid	seeQTL
rs5002947	ADAMTS4	cis	parietal	SCAN
rs5002947	OLFML2B	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160574000-160578800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:160575600-160584000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:160576000-160579000	Enhancers	Liver	Liver
4	chr1:160576000-160580200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:160576200-160591400	Weak transcription	Spleen	Spleen
6	chr1:160576400-160584800	Genic enhancers	Fetal Thymus	thymus
7	chr1:160576800-160591400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:160577000-160580200	Weak transcription	Fetal Intestine Large	intestine
9	chr1:160577000-160580400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:160577000-160580800	Weak transcription	Fetal Intestine Small	intestine
11	chr1:160577000-160581000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
12	chr1:160577000-160584200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:160577000-160590800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:160577200-160579200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:160577200-160584400	Genic enhancers	Thymus	Thymus
16	chr1:160577400-160578800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:160577400-160579000	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr1:160577400-160584200	Strong transcription	Primary T cells from cord blood	blood
19	chr1:160577600-160578200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:160577600-160578400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:160577600-160579000	Genic enhancers	GM12878-XiMat	blood
22	chr1:160577600-160579600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr1:160577600-160580200	Weak transcription	Dnd41	blood
24	chr1:160577600-160580200	Weak transcription	K562	blood
25	chr1:160577600-160580600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:160577600-160584400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr1:160577800-160578800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:160577800-160579000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:160577800-160580000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:160577800-160583200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:160578000-160580200	Weak transcription	Primary B cells from cord blood	blood
32	chr1:160578000-160587400	Strong transcription	Primary B cells from peripheral blood	blood

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