Variant report

Variant	rs9379703
Chromosome Location	chr6:24992226-24992227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24855976..24856788-chr6:24991509..24992791,3	MCF-7	breast:
2	chr6:24855936..24856490-chr6:24992134..24992789,3	K562	blood:
3	chr6:24856039..24856860-chr6:24991781..24992759,3	MCF-7	breast:
4	chr6:24933973..24934661-chr6:24991849..24992763,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10946738	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs13192546	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13209866	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs450392	0.84[CHD][hapmap]
rs62401115	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67879608	0.88[AFR][1000 genomes]
rs742953	0.88[AFR][1000 genomes]
rs9295637	0.88[AFR][1000 genomes]
rs9348651	0.81[AFR][1000 genomes]
rs9348652	0.82[AFR][1000 genomes]
rs9348653	0.88[AFR][1000 genomes]
rs9356950	0.81[JPT][hapmap]
rs9356951	0.81[JPT][hapmap]
rs9358809	0.88[AFR][1000 genomes]
rs9358810	0.81[AFR][1000 genomes]
rs9358811	0.81[JPT][hapmap];0.92[AFR][1000 genomes]
rs9358813	0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9366588	0.88[AFR][1000 genomes]
rs9366590	0.81[JPT][hapmap]
rs9379701	0.81[JPT][hapmap];0.92[AFR][1000 genomes]
rs9379702	0.92[AFR][1000 genomes]
rs9379704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393596	0.88[AFR][1000 genomes]
rs9393597	0.87[ASW][hapmap];0.81[AFR][1000 genomes]
rs9393598	0.92[AFR][1000 genomes]
rs9393599	0.81[JPT][hapmap]
rs9393602	0.86[JPT][hapmap]
rs9393603	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1019504	chr6:24869174-24994758	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9379703	HIST1H2BK	cis	parietal	SCAN
rs9379703	LRRC16A	cis	lymphoblastoid	seeQTL
rs9379703	ZSCAN16	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24984200-24995200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:24986000-24996600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:24986400-24992800	Enhancers	Primary B cells from peripheral blood	blood
4	chr6:24986400-24995200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:24986400-24995400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr6:24986600-24996600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:24987600-25000200	Weak transcription	Lung	lung
8	chr6:24990000-24992800	Enhancers	Primary T cells fromperipheralblood	blood
9	chr6:24990400-24992600	Enhancers	Fetal Heart	heart
10	chr6:24990400-24992600	Enhancers	Hela-S3	cervix
11	chr6:24990400-24992600	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr6:24990400-24992800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:24990400-24993800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:24990600-24992600	Enhancers	Primary hematopoietic stem cells	blood
15	chr6:24990600-24992600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:24990600-24992800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr6:24990600-24993000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr6:24991000-24992400	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr6:24991200-24992400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:24991200-24992600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr6:24991200-24992600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr6:24991200-24992600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr6:24991400-24992800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:24991800-24992400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr6:24991800-24992600	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr6:24991800-24992600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr6:24992000-24992400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr6:24992000-24992600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr6:24992000-24992600	Enhancers	H1 Cell Line	embryonic stem cell
30	chr6:24992000-24992600	Enhancers	H9 Cell Line	embryonic stem cell
31	chr6:24992000-24992600	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr6:24992000-24992600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr6:24992000-24992800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:24992000-24992800	Enhancers	Dnd41	blood
35	chr6:24992200-24992600	Enhancers	Primary B cells from cord blood	blood
36	chr6:24992200-24992600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr6:24992200-24992600	Enhancers	GM12878-XiMat	blood
38	chr6:24992200-24992800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr6:24992200-24992800	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr6:24992200-24993000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr6:24992200-24995200	Weak transcription	Thymus	Thymus
42	chr6:24992200-24995600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:24992200-24996600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:24992200-24996600	Weak transcription	Fetal Thymus	thymus
45	chr6:24992200-24996600	Weak transcription	Stomach Mucosa	stomach
46	chr6:24992200-24998000	Weak transcription	Fetal Muscle Leg	muscle
47	chr6:24992200-25006800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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