Variant report

Variant	rs970741
Chromosome Location	chr1:169480045-169480046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:169475668..169477747-chr1:169479800..169482071,3	MCF-7	breast:
2	chr1:169452842..169455607-chr1:169476881..169480160,5	K562	blood:
3	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
4	chr1:169461586..169463746-chr1:169479948..169481898,2	MCF-7	breast:
5	chr1:169452842..169460813-chr1:169474364..169480814,10	K562	blood:
6	chr1:169478952..169480932-chr1:169498032..169500995,2	MCF-7	breast:
7	chr1:169451858..169456935-chr1:169476541..169486862,15	MCF-7	breast:
8	chr1:169477985..169481647-chr1:169506965..169511270,5	MCF-7	breast:
9	chr1:169474592..169479041-chr1:169479760..169483418,4	K562	blood:
10	chr1:169476802..169481525-chr1:169483770..169486854,5	K562	blood:
11	chr1:169480009..169482936-chr1:169495810..169499823,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000198734	Chromatin interaction
ENSG00000213062	Chromatin interaction
ENSG00000117479	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10800450	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10800453	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10919178	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10919186	0.80[LWK][hapmap]
rs1121789	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11579441	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12127364	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1557570	0.80[CEU][hapmap];0.84[CHB][hapmap]
rs2009814	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2187952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2187953	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2213866	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2213867	0.82[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2239851	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2420373	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766103	0.92[CHB][hapmap]
rs3766109	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766110	0.83[GIH][hapmap];0.80[LWK][hapmap]
rs3820060	0.88[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.90[YRI][hapmap];0.82[ASN][1000 genomes]
rs4524	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4525	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656185	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4656187	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4656684	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656685	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6016	0.95[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6017	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6021	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6030	0.83[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][hapmap];0.82[MKK][hapmap]
rs6032	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6662593	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6662696	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6670393	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6675244	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6701330	0.81[CEU][hapmap];0.84[CHB][hapmap]
rs9287090	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9287092	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9332595	0.83[GIH][hapmap];0.83[LWK][hapmap]
rs9332600	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9332619	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332620	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9332627	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9332635	1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9332643	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9332651	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9332653	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs9332655	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9332665	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.82[ASN][1000 genomes]
rs9332667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs970741	XCL2	cis	cerebellum	SCAN
rs970741	GPR161	cis	parietal	SCAN
rs970741	CREG1	cis	parietal	SCAN
rs970741	C1orf112	cis	parietal	SCAN
rs970741	DCAF6	cis	parietal	SCAN
rs970741	RXRG	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169475800-169481600	Enhancers	Liver	Liver
2	chr1:169477600-169481200	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr1:169477800-169482600	Weak transcription	Placenta	Placenta
4	chr1:169477800-169482600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:169478000-169482600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr1:169478200-169480600	Enhancers	HepG2	liver
7	chr1:169478200-169481800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr1:169478200-169482600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:169478200-169487000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:169478400-169480400	Weak transcription	A549	lung
11	chr1:169478400-169481400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:169478600-169480800	Enhancers	HSMM	muscle
13	chr1:169478600-169481400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:169478600-169482600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:169478600-169482600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:169478800-169480200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:169478800-169482000	Weak transcription	Adipose Nuclei	Adipose
18	chr1:169478800-169482600	Weak transcription	Fetal Lung	lung
19	chr1:169478800-169484000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:169478800-169488200	Weak transcription	Small Intestine	intestine
21	chr1:169479400-169481000	Enhancers	Stomach Mucosa	stomach
22	chr1:169479400-169482600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr1:169479400-169485000	Enhancers	Hela-S3	cervix
24	chr1:169479600-169481400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:169479600-169482600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:169479800-169480200	Weak transcription	HUVEC	blood vessel
27	chr1:169479800-169481400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:169480000-169480600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:169480000-169480800	Enhancers	NHLF	lung
30	chr1:169480000-169481400	Enhancers	NHDF-Ad	bronchial
31	chr1:169480000-169482000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:169480000-169482000	Enhancers	HMEC	breast
33	chr1:169480000-169483000	Enhancers	Muscle Satellite Cultured Cells	--

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