Variant report

Variant	rs9358927
Chromosome Location	chr6:26330492-26330493
allele	G/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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26286019..26289232-chr6:26328153..26331757,3	MCF-7	breast:
2	chr6:26329307..26333799-chr6:26568024..26573999,9	K562	blood:
3	chr6:26327533..26330637-chr6:27103047..27105272,3	K562	blood:
4	chr6:26216015..26217608-chr6:26329315..26332026,2	MCF-7	breast:
5	chr6:26327970..26330676-chr6:26575820..26578738,2	K562	blood:
6	chr6:26327903..26334280-chr6:26553526..26557732,8	K562	blood:
7	chr6:26330167..26332009-chr6:26561007..26562531,2	K562	blood:
8	chr6:26329309..26333130-chr6:26553526..26558565,5	K562	blood:
9	chr6:26329107..26333235-chr6:26529334..26532709,3	K562	blood:
10	chr6:26201103..26202620-chr6:26329166..26330912,2	MCF-7	breast:
11	chr6:26328637..26334167-chr6:26519696..26523328,10	K562	blood:
12	chr6:26330362..26332555-chr6:26595064..26597595,2	MCF-7	breast:
13	chr6:26328486..26331795-chr6:26519848..26525412,6	K562	blood:
14	chr6:26328431..26333737-chr6:26535954..26540361,8	K562	blood:
15	chr6:26328751..26331113-chr6:26570899..26573999,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228223	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000217275	Chromatin interaction
ENSG00000182952	Chromatin interaction
ENSG00000168274	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1053860	0.83[JPT][hapmap]
rs10946810	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs11751978	0.81[JPT][hapmap]
rs11752014	0.81[JPT][hapmap]
rs11755943	0.90[JPT][hapmap]
rs11759682	0.90[JPT][hapmap]
rs11759720	0.90[JPT][hapmap]
rs12525187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12660432	0.81[EUR][1000 genomes]
rs12665035	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs16891523	0.81[JPT][hapmap]
rs16891525	0.81[JPT][hapmap]
rs17608582	0.81[EUR][1000 genomes]
rs1883213	0.92[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs1883214	0.81[JPT][hapmap]
rs1987244	0.81[EUR][1000 genomes]
rs1997768	0.90[JPT][hapmap]
rs2893820	0.92[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs2893842	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs2893843	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3734533	0.90[JPT][hapmap]
rs3778279	0.83[JPT][hapmap]
rs3823157	0.90[JPT][hapmap]
rs4412193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4631273	0.81[JPT][hapmap]
rs61324092	0.81[EUR][1000 genomes]
rs62394764	0.80[EUR][1000 genomes]
rs62394768	0.82[EUR][1000 genomes]
rs6901243	0.90[JPT][hapmap]
rs6908402	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6914596	0.81[JPT][hapmap]
rs6917995	0.80[ASN][1000 genomes]
rs6918325	0.81[EUR][1000 genomes]
rs6930616	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs725575	0.80[EUR][1000 genomes]
rs7755741	0.81[CEU][hapmap];0.91[JPT][hapmap]
rs9357005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9358914	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs9358916	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9358918	0.91[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9358920	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9358925	0.92[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs9358926	0.84[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs9366648	0.88[CEU][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap]
rs9366650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9379842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9379844	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9379846	0.81[EUR][1000 genomes]
rs9393691	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9393693	1.00[YRI][hapmap]
rs9393696	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9393697	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs994379	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
6	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
7	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	nsv5230	chr6:26321593-26361531	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9358927	HIST1H4H	cis	cerebellum	SCAN
rs9358927	WDR90	trans	parietal	SCAN
rs9358927	ACOT13	cis	cerebellum	SCAN
rs9358927	HIST1H3C	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26322800-26331200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:26326600-26332800	Active TSS	A549	lung
3	chr6:26327000-26331800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:26327200-26333000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:26327400-26331000	Active TSS	NHEK	skin
6	chr6:26327800-26330800	Active TSS	HepG2	liver
7	chr6:26328200-26331000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:26328200-26331000	Weak transcription	HSMM	muscle
9	chr6:26328400-26331000	Bivalent Enhancer	Primary T cells from cord blood	blood
10	chr6:26328800-26330600	Weak transcription	HMEC	breast
11	chr6:26328800-26330800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:26329000-26330600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:26329000-26330600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:26329000-26330600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:26329000-26330600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:26329000-26330600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:26329000-26330600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:26329000-26330600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr6:26329000-26330800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:26329000-26331000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:26329000-26331000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:26329200-26330600	Weak transcription	NH-A	brain
23	chr6:26329400-26330600	Weak transcription	NHLF	lung
24	chr6:26329400-26330600	Enhancers	Osteobl	bone
25	chr6:26329400-26330800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
26	chr6:26329600-26331600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
27	chr6:26329600-26331600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
28	chr6:26329600-26333200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:26329800-26331200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
30	chr6:26330000-26330800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
31	chr6:26330000-26330800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:26330000-26333400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr6:26330200-26330600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:26330200-26330800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:26330200-26331000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:26330200-26331400	Enhancers	Placenta Amnion	Placenta Amnion
37	chr6:26330200-26332000	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr6:26330200-26332000	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr6:26330200-26333200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:26330200-26333400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
41	chr6:26330400-26330600	Bivalent/Poised TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr6:26330400-26330600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
43	chr6:26330400-26330600	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr6:26330400-26330600	Bivalent Enhancer	Psoas Muscle	Psoas
45	chr6:26330400-26330600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
46	chr6:26330400-26330600	Active TSS	GM12878-XiMat	blood
47	chr6:26330400-26330800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
48	chr6:26330400-26331000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:26330400-26331000	Bivalent Enhancer	Fetal Heart	heart
50	chr6:26330400-26331000	Bivalent Enhancer	Fetal Intestine Small	intestine

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