Variant report

Variant	rs6909762
Chromosome Location	chr6:25962044-25962045
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:44)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:44 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:25962040-25962190	GM12871	blood:	n/a	n/a
2	RAD21	chr6:25961967-25962218	HepG2	liver:	n/a	n/a
3	CTCF	chr6:25962034-25962251	HepG2	liver:	n/a	n/a
4	CTCF	chr6:25962040-25962190	GM12873	blood:	n/a	n/a
5	CTCF	chr6:25961900-25962050	HUVEC	blood vessel:	n/a	n/a
6	CTCF	chr6:25962020-25962170	GM12875	blood:	n/a	n/a
7	CTCF	chr6:25961991-25962745	K562	blood:	n/a	n/a
8	CTCF	chr6:25961980-25962130	BJ	skin:	n/a	n/a
9	CTCF	chr6:25962040-25962190	HMF	breast:	n/a	n/a
10	CTCF	chr6:25962020-25962170	HCPEpiC	choroid plexus:	n/a	n/a
11	CTCF	chr6:25962040-25962190	HCPEpiC	choroid plexus:	n/a	n/a
12	CTCF	chr6:25962020-25962170	GM12873	blood:	n/a	n/a
13	CTCF	chr6:25962040-25962190	GM12870	blood:	n/a	n/a
14	CTCF	chr6:25961989-25962340	GM12878	blood:	n/a	n/a
15	RAD21	chr6:25961992-25962208	K562	blood:	n/a	n/a
16	CTCF	chr6:25962040-25962190	HRPEpiC	eye:	n/a	n/a
17	RAD21	chr6:25961984-25962266	H1-hESC	embryonic stem cell:	n/a	n/a
18	ZNF143	chr6:25961993-25963231	GM12878	blood:	n/a	chr6:25962903-25962912
19	RAD21	chr6:25961978-25962308	GM12878	blood:	n/a	n/a
20	CTCF	chr6:25961805-25962194	GM19238	blood:	n/a	n/a
21	CHD2	chr6:25961992-25962116	HepG2	liver:	n/a	n/a
22	CTCF	chr6:25961980-25962130	GM06990	blood:	n/a	n/a
23	POLR2A	chr6:25961698-25964844	GM12891	blood:	n/a	n/a
24	CTCF	chr6:25962020-25962170	Hela-S3	cervix:	n/a	n/a
25	RAD21	chr6:25961707-25962340	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr6:25962040-25962190	AoAF	blood vessel:	n/a	n/a
27	RAD21	chr6:25962034-25962244	Hela-S3	cervix:	n/a	n/a
28	RAD21	chr6:25961952-25962218	H1-hESC	embryonic stem cell:	n/a	n/a
29	RAD21	chr6:25961994-25962299	HepG2	liver:	n/a	n/a
30	CTCF	chr6:25962000-25962150	HEK293	kidney:	n/a	n/a
31	CTCF	chr6:25962040-25962190	GM12872	blood:	n/a	n/a
32	CTCF	chr6:25962000-25962150	AG04450	lung:	n/a	n/a
33	MTA3	chr6:25961955-25964175	GM12878	blood:	n/a	n/a
34	RAD21	chr6:25961993-25962346	HepG2	liver:	n/a	n/a
35	CTCF	chr6:25962000-25962150	GM12864	blood:	n/a	n/a
36	CTCF	chr6:25962040-25962190	AG09319	gingival:	n/a	n/a
37	CTCF	chr6:25961940-25962090	GM12866	blood:	n/a	n/a
38	CTCF	chr6:25962020-25962170	AG10803	skin:	n/a	n/a
39	BHLHE40	chr6:25961966-25962221	K562	blood:	n/a	n/a
40	CTCF	chr6:25962020-25962170	GM12865	blood:	n/a	n/a
41	CTCF	chr6:25962020-25962170	HepG2	liver:	n/a	n/a
42	CTCF	chr6:25962020-25962170	NB4	blood:	n/a	n/a
43	CTCF	chr6:25962020-25962170	HCM	heart:	n/a	n/a
44	CTCF	chr6:25961940-25962090	A549	lung:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25962020..25964518-chr6:25991024..25993046,2	MCF-7	breast:
2	chr6:25961783..25964529-chr6:25992813..25995946,4	MCF-7	breast:

No data

Variant related genes	Relation type
TRIM38	TF binding region
ENSG00000272462	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1078542	1.00[EUR][1000 genomes]
rs1090949	1.00[TSI][hapmap]
rs199757	1.00[TSI][hapmap]
rs58764905	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60902216	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs62625349	0.87[AFR][1000 genomes]
rs6940331	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs736088	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs807203	1.00[TSI][hapmap]
rs807211	1.00[TSI][hapmap]
rs807213	1.00[TSI][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	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	esv2755446	chr6:25924513-25981648	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv432857	chr6:25957109-26072445	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	451 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25956000-25963000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:25958400-25962200	Enhancers	Primary B cells from peripheral blood	blood
3	chr6:25959000-25962200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
4	chr6:25959600-25962200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr6:25959600-25962400	Enhancers	Fetal Muscle Leg	muscle
6	chr6:25959800-25962200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr6:25959800-25962200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr6:25959800-25962200	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr6:25960600-25962200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr6:25960600-25962400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:25960800-25962200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:25960800-25962200	Enhancers	GM12878-XiMat	blood
13	chr6:25960800-25962400	Weak transcription	Psoas Muscle	Psoas
14	chr6:25961000-25962200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr6:25961200-25962200	Enhancers	HSMMtube	muscle
16	chr6:25961600-25962200	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr6:25961600-25962200	Enhancers	Primary T cells from cord blood	blood
18	chr6:25961600-25962400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr6:25961600-25962800	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr6:25961600-25963000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:25961800-25962200	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:25961800-25962200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:25961800-25962200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:25961800-25962200	Enhancers	Adipose Nuclei	Adipose
25	chr6:25961800-25962200	Enhancers	Gastric	stomach
26	chr6:25961800-25962400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:25961800-25962400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:25961800-25962400	Enhancers	Fetal Muscle Trunk	muscle
29	chr6:25961800-25962400	Enhancers	Right Atrium	heart
30	chr6:25961800-25962400	Enhancers	HUVEC	blood vessel
31	chr6:25961800-25962600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:25961800-25962600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:25961800-25962600	Flanking Active TSS	Colon Smooth Muscle	Colon
34	chr6:25961800-25962600	Enhancers	Lung	lung
35	chr6:25961800-25962800	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr6:25961800-25962800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr6:25961800-25962800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr6:25961800-25962800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr6:25961800-25962800	Enhancers	Small Intestine	intestine
40	chr6:25961800-25962800	Enhancers	Spleen	Spleen
41	chr6:25961800-25962800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr6:25961800-25963000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
43	chr6:25961800-25963000	Flanking Active TSS	Dnd41	blood
44	chr6:25962000-25962200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:25962000-25962200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:25962000-25962200	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr6:25962000-25962200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:25962000-25962200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:25962000-25962200	Flanking Active TSS	Colonic Mucosa	Colon
50	chr6:25962000-25962200	Weak transcription	Fetal Lung	lung

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