Variant report

Variant	rs9379750
Chromosome Location	chr6:25266147-25266148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:25266060-25266210	GM12875	blood:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
2	CTCF	chr6:25266020-25266170	RPTEC	kidney:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
3	CTCF	chr6:25266000-25266270	A549	lung:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
4	CTCF	chr6:25266020-25266170	HCM	heart:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
5	CTCF	chr6:25266000-25266150	GM12872	blood:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
6	CTCF	chr6:25265959-25266216	LNCaP	prostate:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
7	RAD21	chr6:25265795-25266417	MCF-7	breast:	n/a	chr6:25266094-25266106 chr6:25266089-25266108
8	CTCF	chr6:25265965-25266216	Lung_OC	lung:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
9	CTCF	chr6:25266000-25266150	BJ	skin:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
10	CTCF	chr6:25265947-25266241	K562	blood:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
11	CTCF	chr6:25266020-25266170	HEEpiC	esophagus:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
12	RAD21	chr6:25265908-25266329	GM12878	blood:	n/a	chr6:25266094-25266106 chr6:25266089-25266108
13	CTCF	chr6:25266040-25266190	GM12872	blood:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
14	CTCF	chr6:25266020-25266208	A549	lung:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
15	CTCF	chr6:25265876-25266261	K562	blood:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
16	CTCF	chr6:25266060-25266210	HAc	cerebellar:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
17	CTCF	chr6:25266040-25266190	HMF	breast:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
18	RAD21	chr6:25265801-25266292	H1-hESC	embryonic stem cell:	n/a	chr6:25266094-25266106 chr6:25266089-25266108
19	CTCF	chr6:25266040-25266190	HCM	heart:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
20	CTCF	chr6:25266000-25266150	AG04449	skin:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
21	SMC3	chr6:25265931-25266253	K562	blood:	n/a	chr6:25266090-25266104
22	RAD21	chr6:25265821-25266427	A549	lung:	n/a	chr6:25266094-25266106 chr6:25266089-25266108
23	CTCF	chr6:25266000-25266150	HEEpiC	esophagus:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
24	CTCF	chr6:25266000-25266150	Caco-2	colon:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
25	CTCF	chr6:25265948-25266228	Pancreas_OC	pancreas:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
26	CTCF	chr6:25266020-25266170	GM12865	blood:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
27	CTCF	chr6:25266000-25266150	BE2_C	brain:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
28	CTCF	chr6:25266000-25266150	HEK293	kidney:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
29	CTCF	chr6:25266020-25266170	AoAF	blood vessel:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
30	CTCF	chr6:25265934-25266245	HUVEC	blood vessel:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
31	CTCF	chr6:25266020-25266170	HL-60	blood:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
32	MAFK	chr6:25265967-25266814	HepG2	liver:	n/a	chr6:25266644-25266653 chr6:25266642-25266658 chr6:25266643-25266657 chr6:25266647-25266656 chr6:25266640-25266660 chr6:25266646-25266656
33	CTCF	chr6:25265921-25266253	Spleen_OC	spleen:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
34	CTCF	chr6:25266060-25266210	WERI-Rb-1	eye:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
35	CTCF	chr6:25265778-25266515	HCT-116	colon:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
36	CTCF	chr6:25265947-25266243	GM12878	blood:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
37	STAT3	chr6:25265938-25266238	MCF10A-Er-Src	breast:	n/a	n/a
38	RAD21	chr6:25265802-25266408	MCF-7	breast:	n/a	chr6:25266094-25266106 chr6:25266089-25266108
39	CTCF	chr6:25266020-25266170	GM12864	blood:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
40	CTCF	chr6:25266040-25266190	HFF-Myc	foreskin:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
41	CTCF	chr6:25266040-25266190	Hela-S3	cervix:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
42	CTCF	chr6:25265935-25266236	MCF-7	breast:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
43	RAD21	chr6:25265796-25266346	HepG2	liver:	n/a	chr6:25266094-25266106 chr6:25266089-25266108
44	CTCF	chr6:25266040-25266190	A549	lung:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
45	CTCF	chr6:25265864-25266311	GM12878	blood:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
46	CTCF	chr6:25265929-25266243	Medullo	brain:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
47	CTCF	chr6:25266020-25266170	HCT-116	colon:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
48	CTCF	chr6:25266020-25266170	AG04449	skin:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
49	CTCF	chr6:25266000-25266150	SAEC	small airway:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104
50	CTCF	chr6:25266000-25266150	HRPEpiC	eye:	n/a	chr6:25266090-25266111 chr6:25266089-25266105 chr6:25266088-25266106 chr6:25266091-25266104

No.	Distal block	Cell Line	Cell type
1	chr6:25266023..25266919-chr6:25278956..25279656,2	MCF-7	breast:
2	chr6:25266060..25267780-chr6:26028723..26030730,2	K562	blood:
3	chr6:25265932..25266579-chr6:25556462..25557180,3	MCF-7	breast:
4	chr6:25264842..25266503-chr6:25491535..25493779,2	MCF-7	breast:
5	chr6:25265692..25268532-chr6:25269921..25272055,2	MCF-7	breast:
6	chr6:25265953..25268779-chr6:25278296..25280757,3	MCF-7	breast:
7	chr6:25265792..25266348-chr6:25490241..25490927,2	K562	blood:
8	chr6:25265686..25266899-chr6:25490019..25490918,5	MCF-7	breast:
9	chr6:25223636..25224166-chr6:25265963..25266626,2	MCF-7	breast:
10	chr6:25265655..25266620-chr6:25556304..25557308,7	K562	blood:

Variant related genes	Relation type
ENSG00000235733	TF binding region
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1016854	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1016855	0.91[CEU][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs2050044	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2064211	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2078527	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2690067	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2744254	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2744267	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs2744268	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs6914799	0.88[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs6926126	0.88[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs721036	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs723047	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7748256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9356971	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9356972	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9358849	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9366614	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393636	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393637	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	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
2	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv883483	chr6:25200842-25272435	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9379750	LENG9	trans	cerebellum	SCAN
rs9379750	ZNF192	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25264200-25266200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:25264600-25266200	Weak transcription	Osteobl	bone
3	chr6:25265800-25266200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:25265800-25266200	Enhancers	Primary T cells from cord blood	blood
5	chr6:25265800-25266200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:25265800-25266400	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr6:25265800-25266400	Enhancers	Adipose Nuclei	Adipose
8	chr6:25265800-25267200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:25265800-25267400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:25265800-25267400	Enhancers	NHDF-Ad	bronchial
11	chr6:25266000-25266400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:25266000-25266400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:25266000-25266400	Enhancers	Fetal Kidney	kidney
14	chr6:25266000-25266400	Enhancers	Fetal Lung	lung
15	chr6:25266000-25266800	Enhancers	Cortex derived primary cultured neurospheres	brain

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