Variant report

Variant	rs11965377
Chromosome Location	chr6:27279877-27279878
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	MAX	chr6:27279507-27280190	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr6:27279479-27280881	A549	lung:	n/a	n/a
3	SMC3	chr6:27279813-27280962	SK-N-SH	brain:	n/a	chr6:27280635-27280649
4	ELF1	chr6:27279673-27280871	GM12878	blood:	n/a	chr6:27280597-27280608
5	CTCF	chr6:27279760-27279910	GM12864	blood:	n/a	n/a
6	E2F6	chr6:27279351-27280833	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr6:27279600-27280114	H1-hESC	embryonic stem cell:	n/a	n/a
8	USF1	chr6:27279540-27279939	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr6:27279554-27280893	H1-hESC	embryonic stem cell:	n/a	chr6:27280634-27280653
10	CTCF	chr6:27279860-27280010	GM12867	blood:	n/a	n/a
11	SIN3A	chr6:27279775-27280838	H1-hESC	embryonic stem cell:	n/a	n/a
12	E2F6	chr6:27279160-27280852	H1-hESC	embryonic stem cell:	n/a	n/a
13	CHD2	chr6:27279689-27280725	H1-hESC	embryonic stem cell:	n/a	chr6:27280236-27280246 chr6:27280271-27280281
14	USF1	chr6:27279533-27279954	H1-hESC	embryonic stem cell:	n/a	n/a
15	MXI1	chr6:27279615-27279878	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr6:27279678-27280859	A549	lung:	n/a	n/a
17	CTCF	chr6:27279844-27281161	A549	lung:	n/a	chr6:27280633-27280651 chr6:27280635-27280656
18	MAX	chr6:27279457-27280837	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr6:27279426-27280863	H1-hESC	embryonic stem cell:	n/a	n/a
20	RAD21	chr6:27279877-27280900	H1-hESC	embryonic stem cell:	n/a	chr6:27280634-27280653
21	CTCF	chr6:27279876-27281039	SK-N-SH	brain:	n/a	chr6:27280633-27280651 chr6:27280635-27280656
22	E2F6	chr6:27279630-27280796	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27279187..27280995-chr6:27439360..27441808,2	MCF-7	breast:
2	chr6:27114741..27116846-chr6:27278241..27280578,2	K562	blood:

Variant related genes	Relation type
POM121L2	TF binding region
ENSG00000265565	Chromatin interaction
ENSG00000096654	Chromatin interaction
ENSG00000184825	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1102568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11753248	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11754166	1.00[ASN][1000 genomes]
rs11756458	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757216	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11757320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11961333	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11962403	1.00[ASN][1000 genomes]
rs11962826	1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11965529	1.00[ASN][1000 genomes]
rs11966553	1.00[ASN][1000 genomes]
rs11966985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11967073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11967759	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11969536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11970261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2021277	1.00[ASN][1000 genomes]
rs2893912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34979454	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800316	1.00[CHB][hapmap]
rs6904118	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6918648	1.00[MEX][hapmap]
rs73738797	1.00[ASN][1000 genomes]
rs73740408	1.00[ASN][1000 genomes]
rs7744248	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7759741	1.00[CHB][hapmap]
rs858978	1.00[ASN][1000 genomes]
rs858979	1.00[ASN][1000 genomes]
rs858983	1.00[CEU][hapmap]
rs9969094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv883506	chr6:27271343-27288687	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27279400-27280000	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:27279400-27280600	Active TSS	Gastric	stomach
3	chr6:27279400-27281000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr6:27279400-27281000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr6:27279400-27281000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr6:27279400-27281000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:27279600-27280000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:27279600-27280000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:27279600-27280000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:27279600-27280000	Bivalent Enhancer	Colon Smooth Muscle	Colon
11	chr6:27279600-27280000	Bivalent Enhancer	Fetal Muscle Leg	muscle
12	chr6:27279600-27280000	Bivalent Enhancer	Placenta	Placenta
13	chr6:27279600-27280000	Bivalent Enhancer	Left Ventricle	heart
14	chr6:27279600-27280000	Bivalent Enhancer	Lung	lung
15	chr6:27279600-27280200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:27279600-27280200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
17	chr6:27279600-27280200	Enhancers	Spleen	Spleen
18	chr6:27279600-27280400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr6:27279600-27280600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr6:27279600-27280600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:27279600-27280800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:27279600-27280800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr6:27279600-27280800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:27279600-27281000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr6:27279600-27281000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr6:27279600-27281000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:27279800-27280000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:27279800-27280000	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:27279800-27280000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:27279800-27280000	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
31	chr6:27279800-27280000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
32	chr6:27279800-27280000	Bivalent Enhancer	Primary B cells from cord blood	blood
33	chr6:27279800-27280000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
34	chr6:27279800-27280000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
35	chr6:27279800-27280000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:27279800-27280000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
37	chr6:27279800-27280000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:27279800-27280000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
39	chr6:27279800-27280000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr6:27279800-27280000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
41	chr6:27279800-27280000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:27279800-27280000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
43	chr6:27279800-27280000	Bivalent Enhancer	Liver	Liver
44	chr6:27279800-27280000	Bivalent Enhancer	Brain Angular Gyrus	brain
45	chr6:27279800-27280000	Bivalent Enhancer	Brain Cingulate Gyrus	brain
46	chr6:27279800-27280000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
47	chr6:27279800-27280000	Bivalent Enhancer	Brain Substantia Nigra	brain
48	chr6:27279800-27280000	Enhancers	Esophagus	oesophagus
49	chr6:27279800-27280000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
50	chr6:27279800-27280000	Bivalent/Poised TSS	Fetal Intestine Large	intestine

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