Variant report

Variant	rs12665144
Chromosome Location	chr6:39083288-39083289
allele	C/T
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	MAFK	chr6:39082144-39083484	Hela-S3	cervix:	n/a	n/a
2	RCOR1	chr6:39082051-39083337	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr6:39082264-39083338	GM18951	blood:	n/a	n/a
4	USF2	chr6:39082608-39083429	H1-hESC	embryonic stem cell:	n/a	chr6:39082939-39082955
5	CTCF	chr6:39083140-39083290	HPF	lung:	n/a	n/a
6	HDAC2	chr6:39082279-39083376	MCF-7	breast:	n/a	n/a
7	MAZ	chr6:39082155-39083386	K562	blood:	n/a	chr6:39083069-39083076
8	CTCF	chr6:39083240-39083390	BJ	skin:	n/a	n/a
9	HCFC1	chr6:39082263-39083486	K562	blood:	n/a	n/a
10	POLR2A	chr6:39082124-39083538	K562	blood:	n/a	n/a
11	TCF7L2	chr6:39082436-39083305	HCT-116	colon:	n/a	n/a
12	CTCF	chr6:39083180-39083330	K562	blood:	n/a	n/a
13	GTF2F1	chr6:39082099-39083402	Hela-S3	cervix:	n/a	n/a
14	REST	chr6:39082147-39083424	HL-60	blood:	n/a	chr6:39082616-39082629 chr6:39082934-39082947
15	E2F6	chr6:39082328-39083474	H1-hESC	embryonic stem cell:	n/a	chr6:39082957-39082966 chr6:39082899-39082913 chr6:39082557-39082566 chr6:39082941-39082950 chr6:39082823-39082838
16	MAX	chr6:39082070-39083532	HCT-116	colon:	n/a	chr6:39083069-39083076 chr6:39083066-39083076
17	POLR2A	chr6:39082327-39083315	PFSK-1	brain:	n/a	n/a
18	CTCF	chr6:39083100-39083330	RPTEC	kidney:	n/a	n/a
19	MAX	chr6:39082262-39083365	H1-hESC	embryonic stem cell:	n/a	chr6:39083069-39083076 chr6:39083066-39083076
20	MAX	chr6:39082081-39083491	MCF-7	breast:	n/a	chr6:39083069-39083076 chr6:39083066-39083076
21	GATA3	chr6:39082267-39083444	MCF-7	breast:	n/a	chr6:39083329-39083350 chr6:39083332-39083348
22	RELA	chr6:39082327-39083298	GM15510	blood:	n/a	n/a
23	POLR2A	chr6:39082167-39083351	GM12878	blood:	n/a	n/a
24	CHD2	chr6:39082395-39083296	K562	blood:	n/a	n/a
25	CHD2	chr6:39082024-39083337	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr6:39082048-39083466	GM12878	blood:	n/a	n/a
27	GATA2	chr6:39082221-39083364	SH-SY5Y	brain:	n/a	chr6:39083329-39083350 chr6:39083332-39083348
28	POLR2A	chr6:39082106-39083698	MCF10A-Er-Src	breast:	n/a	n/a
29	MAFK	chr6:39082393-39083324	HepG2	liver:	n/a	n/a
30	POLR2A	chr6:39082236-39083328	K562	blood:	n/a	n/a
31	WRNIP1	chr6:39082239-39083361	GM12878	blood:	n/a	n/a
32	EP300	chr6:39082181-39083541	K562	blood:	n/a	chr6:39083142-39083158 chr6:39082944-39082953 chr6:39082937-39082953 chr6:39082941-39082950
33	REST	chr6:39081857-39083293	H1-neurons	neurons:	n/a	chr6:39082616-39082629 chr6:39082934-39082947
34	TCF12	chr6:39082354-39083300	A549	lung:	n/a	n/a
35	MYC	chr6:39082023-39083319	NB4	blood:	n/a	chr6:39083069-39083076 chr6:39083066-39083076
36	CTCF	chr6:39083167-39083289	A549	lung:	n/a	n/a
37	POLR2A	chr6:39082219-39083331	PANC-1	pancreas:	n/a	n/a
38	POLR2A	chr6:39081660-39083848	MCF10A-Er-Src	breast:	n/a	n/a
39	MAX	chr6:39082185-39083545	A549	lung:	n/a	chr6:39083069-39083076 chr6:39083066-39083076
40	MAX	chr6:39082076-39083480	ECC-1	luminal epithelium:	n/a	chr6:39083069-39083076 chr6:39083066-39083076
41	CTCF	chr6:39083129-39083295	MCF-7	breast:	n/a	n/a
42	TAF1	chr6:39082323-39083288	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr6:39082289-39083296	HepG2	liver:	n/a	n/a
44	MAX	chr6:39082132-39083356	GM12878	blood:	n/a	chr6:39083069-39083076 chr6:39083066-39083076
45	POLR2A	chr6:39082158-39083484	K562	blood:	n/a	n/a
46	CTCF	chr6:39083125-39083297	MCF-7	breast:	n/a	n/a
47	POLR2A	chr6:39082003-39083336	PBDE	blood:	n/a	n/a
48	RELA	chr6:39082038-39083353	GM10847	blood:	n/a	n/a
49	MAX	chr6:39081904-39083316	NB4	blood:	n/a	chr6:39083069-39083076 chr6:39083066-39083076
50	E2F6	chr6:39082322-39083510	H1-hESC	embryonic stem cell:	n/a	chr6:39082957-39082966 chr6:39082899-39082913 chr6:39082557-39082566 chr6:39082941-39082950 chr6:39082823-39082838

No.	Distal block	Cell Line	Cell type
1	chr6:39081916..39085282-chr6:39194692..39197671,3	K562	blood:
2	chr6:39081916..39083618-chr6:39195475..39198026,2	K562	blood:
3	chr6:39056771..39059349-chr6:39083061..39085112,2	K562	blood:

Variant related genes	Relation type
SAYSD1	TF binding region
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10305479	1.00[CEU][hapmap]
rs10305516	0.91[CEU][hapmap]
rs10305525	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs1076734	1.00[CEU][hapmap]
rs1077680	1.00[CEU][hapmap]
rs1465570	1.00[ASW][hapmap]
rs2268635	1.00[ASW][hapmap];0.91[CEU][hapmap];0.89[TSI][hapmap]
rs2268636	0.90[CEU][hapmap]
rs2268645	1.00[CEU][hapmap]
rs228819	1.00[ASW][hapmap]
rs2300612	1.00[ASW][hapmap];0.91[CEU][hapmap]
rs2815090	1.00[ASW][hapmap]
rs3765468	0.91[CEU][hapmap]
rs59426516	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs742761	1.00[CEU][hapmap]
rs761387	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39081400-39083400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:39081400-39083600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:39081800-39083400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr6:39081800-39083400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:39081800-39083600	Active TSS	A549	lung
6	chr6:39082000-39083400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:39082000-39083400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:39082000-39083400	Active TSS	Aorta	Aorta
9	chr6:39082000-39083400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr6:39082000-39083600	Flanking Active TSS	Primary B cells from cord blood	blood
11	chr6:39082000-39083600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr6:39082000-39083600	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr6:39082200-39083400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr6:39082200-39083400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:39082200-39083400	Active TSS	Ovary	ovary
16	chr6:39082200-39083400	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr6:39082400-39083400	Active TSS	Brain Anterior Caudate	brain
18	chr6:39082400-39083400	Active TSS	Fetal Kidney	kidney
19	chr6:39082400-39083400	Flanking Active TSS	Fetal Muscle Trunk	muscle
20	chr6:39082400-39083400	Active TSS	Rectal Smooth Muscle	rectum
21	chr6:39082600-39083400	Active TSS	Placenta Amnion	Placenta Amnion
22	chr6:39082800-39083400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:39082800-39083400	Weak transcription	Small Intestine	intestine
24	chr6:39083000-39083400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
25	chr6:39083000-39083400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:39083000-39083400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr6:39083000-39083400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr6:39083000-39083400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:39083000-39083400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:39083000-39083400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:39083000-39083400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:39083000-39083400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
33	chr6:39083000-39083400	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr6:39083000-39083400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr6:39083000-39083400	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr6:39083000-39083400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr6:39083000-39083400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr6:39083000-39083400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr6:39083000-39083400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:39083000-39083400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:39083000-39083400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:39083000-39083400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:39083000-39083400	Flanking Active TSS	Liver	Liver
44	chr6:39083000-39083400	Flanking Active TSS	Colonic Mucosa	Colon
45	chr6:39083000-39083400	Flanking Active TSS	Esophagus	oesophagus
46	chr6:39083000-39083400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr6:39083000-39083400	Flanking Active TSS	Fetal Brain Male	brain
48	chr6:39083000-39083400	Flanking Active TSS	Fetal Intestine Large	intestine
49	chr6:39083000-39083400	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr6:39083000-39083400	Flanking Active TSS	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links