Variant report

Variant	rs7518342
Chromosome Location	chr1:160804934-160804935
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160804559..160806292-chr1:161014093..161016199,2	K562	blood:
2	chr1:160804453..160805506-chr1:160920895..160922480,10	MCF-7	breast:
3	chr1:160804478..160804999-chr1:160923736..160924607,3	K562	blood:
4	chr1:160804510..160805361-chr1:160959406..160960281,2	MCF-7	breast:
5	chr1:160748693..160751200-chr1:160804767..160806895,2	MCF-7	breast:
6	chr1:160804493..160805786-chr1:160920022..160921434,5	MCF-7	breast:
7	chr1:160804431..160805656-chr1:160923714..160924721,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158773	Chromatin interaction
ENSG00000158764	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11265493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11265496	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs11582719	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs11587898	0.84[CEU][hapmap];0.82[AMR][1000 genomes]
rs1319651	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2139660	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2280415	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2779790	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2990702	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2990703	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs3753389	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766379	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4656936	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656937	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs4656938	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs483197	0.88[ASN][1000 genomes]
rs489651	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs491061	0.81[CEU][hapmap]
rs499721	0.91[ASN][1000 genomes]
rs512525	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs535610	0.84[CEU][hapmap];0.84[AMR][1000 genomes]
rs537957	0.84[AMR][1000 genomes]
rs541834	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs549565	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs578608	0.84[AMR][1000 genomes]
rs60755678	0.89[ASN][1000 genomes]
rs6671710	0.84[CEU][hapmap];0.86[AMR][1000 genomes]
rs6682654	0.84[CEU][hapmap];0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv464161	chr1:160747615-160852046	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv548057	chr1:160747615-160852046	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7518342	CD244	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160771000-160806600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:160793000-160811600	Weak transcription	Gastric	stomach
3	chr1:160793400-160807400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:160794000-160805800	Weak transcription	Thymus	Thymus
5	chr1:160794000-160806200	Weak transcription	Spleen	Spleen
6	chr1:160797200-160805000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:160797600-160805000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:160797600-160805200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:160797800-160805600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:160798200-160805000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:160798200-160805000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:160798200-160805000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:160798200-160805600	Weak transcription	Primary B cells from cord blood	blood
14	chr1:160798400-160805000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:160798600-160805600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr1:160799000-160805200	Strong transcription	Primary hematopoietic stem cells	blood
17	chr1:160800800-160805800	Weak transcription	GM12878-XiMat	blood
18	chr1:160802400-160805200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:160803000-160807600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr1:160803200-160805600	Genic enhancers	Primary T cells fromperipheralblood	blood
21	chr1:160803200-160807600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr1:160803200-160812400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:160803400-160806200	Enhancers	Primary T cells from cord blood	blood
24	chr1:160803400-160807400	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr1:160803600-160806000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:160803600-160810000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr1:160803800-160806400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:160804000-160806400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr1:160804000-160807600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:160804400-160807600	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr1:160804600-160805200	Enhancers	Fetal Thymus	thymus
32	chr1:160804600-160807400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:160804800-160805800	Weak transcription	Dnd41	blood
34	chr1:160804800-160809600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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