Variant report

Variant	rs5005
Chromosome Location	chr11:10327547-10327548
allele	C/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	E2F6	chr11:10326936-10327851	A549	lung:	n/a	chr11:10327296-10327311 chr11:10327071-10327082
2	POLR2A	chr11:10325891-10330101	HCT-116	colon:	n/a	n/a
3	CREB1	chr11:10326947-10327606	A549	lung:	n/a	n/a
4	CTBP2	chr11:10326013-10328567	H1-hESC	embryonic stem cell:	n/a	n/a
5	JUND	chr11:10323956-10331669	HCT-116	colon:	n/a	chr11:10326447-10326456 chr11:10331225-10331234 chr11:10326563-10326572 chr11:10331227-10331234 chr11:10324905-10324915 chr11:10329473-10329484 chr11:10331226-10331235 chr11:10329705-10329717 chr11:10329705-10329716 chr11:10331226-10331234 chr11:10329706-10329716 chr11:10330671-10330679 chr11:10329707-10329715 chr11:10329706-10329716 chr11:10329706-10329716 chr11:10331224-10331235
6	USF2	chr11:10327213-10327651	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:10326261-10327890	HUVEC	blood vessel:	n/a	n/a
8	ELF1	chr11:10326230-10328385	GM12878	blood:	n/a	n/a
9	TAF7	chr11:10324386-10331444	H1-hESC	embryonic stem cell:	n/a	n/a
10	HEY1	chr11:10325910-10331758	HepG2	liver:	n/a	chr11:10327166-10327181 chr11:10329744-10329759 chr11:10326566-10326581 chr11:10329041-10329056
11	TAF1	chr11:10325850-10328453	A549	lung:	n/a	n/a
12	CTCF	chr11:10323213-10327582	A549	lung:	n/a	n/a
13	CHD2	chr11:10324029-10327973	Hela-S3	cervix:	n/a	chr11:10327760-10327770 chr11:10327860-10327870 chr11:10326455-10326465 chr11:10326448-10326458
14	POLR2A	chr11:10324106-10328040	HepG2	liver:	n/a	n/a
15	POLR2A	chr11:10326004-10328426	A549	lung:	n/a	n/a
16	ETS1	chr11:10327148-10328547	A549	lung:	n/a	chr11:10327867-10327878 chr11:10327860-10327871
17	POLR2A	chr11:10327534-10327924	GM12878	blood:	n/a	n/a
18	RAD21	chr11:10325502-10330565	SK-N-SH	brain:	n/a	chr11:10326951-10326963 chr11:10329056-10329070 chr11:10329497-10329507 chr11:10329497-10329511 chr11:10329493-10329512 chr11:10326172-10326182
19	SIN3AK20	chr11:10326036-10328003	H1-hESC	embryonic stem cell:	n/a	n/a
20	JUND	chr11:10327384-10328560	A549	lung:	n/a	n/a
21	POLR2A	chr11:10325955-10328644	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr11:10323526-10327709	SK-N-SH	brain:	n/a	n/a
23	SMARCB1	chr11:10326042-10329945	Hela-S3	cervix:	n/a	chr11:10329706-10329715
24	SMC3	chr11:10323716-10327728	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr11:10323851-10331424	HCT-116	colon:	n/a	n/a
26	POLR2A	chr11:10323816-10331549	Hela-S3	cervix:	n/a	n/a
27	TBP	chr11:10325407-10328077	H1-hESC	embryonic stem cell:	n/a	n/a
28	ATF2	chr11:10326418-10331473	H1-hESC	embryonic stem cell:	n/a	n/a
29	RAD21	chr11:10324040-10327869	IMR90	lung:	n/a	chr11:10326951-10326963 chr11:10326172-10326182
30	MAX	chr11:10326059-10327645	SK-N-SH	brain:	n/a	chr11:10326516-10326525
31	CHD2	chr11:10327221-10327916	H1-hESC	embryonic stem cell:	n/a	chr11:10327760-10327770 chr11:10327860-10327870
32	KAP1	chr11:10326622-10328081	HEK293	kidney:	n/a	n/a
33	POLR2A	chr11:10327117-10328645	H1-hESC	embryonic stem cell:	n/a	n/a
34	TFAP2C	chr11:10326033-10328384	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr11:10325942-10330999	HUVEC	blood vessel:	n/a	n/a
36	SIN3AK20	chr11:10323807-10331742	HCT-116	colon:	n/a	n/a
37	POLR2A	chr11:10326058-10328465	HUVEC	blood vessel:	n/a	n/a
38	MAX	chr11:10323478-10330100	A549	lung:	n/a	chr11:10329125-10329138 chr11:10325336-10325345 chr11:10329127-10329134 chr11:10329125-10329138 chr11:10329125-10329138 chr11:10326516-10326525 chr11:10329353-10329363 chr11:10329122-10329141 chr11:10327866-10327876 chr11:10324414-10324425
39	BRCA1	chr11:10327032-10327688	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr11:10323780-10328609	Hela-S3	cervix:	n/a	n/a
41	CHD1	chr11:10322517-10331634	IMR90	lung:	n/a	chr11:10327760-10327770 chr11:10327860-10327870 chr11:10326455-10326465 chr11:10326448-10326458
42	MAX	chr11:10324031-10327826	HepG2	liver:	n/a	chr11:10325336-10325345 chr11:10326516-10326525 chr11:10324414-10324425
43	MAFK	chr11:10323790-10327636	Hela-S3	cervix:	n/a	chr11:10325442-10325451
44	SIN3AK20	chr11:10323960-10328092	HCT-116	colon:	n/a	n/a
45	E2F6	chr11:10326022-10327739	H1-hESC	embryonic stem cell:	n/a	chr11:10326176-10326185 chr11:10327296-10327311 chr11:10326448-10326457 chr11:10327071-10327082 chr11:10326572-10326581 chr11:10326557-10326567
46	RAD21	chr11:10325988-10327968	H1-hESC	embryonic stem cell:	n/a	chr11:10326951-10326963 chr11:10326172-10326182
47	CTCF	chr11:10327440-10327590	HCPEpiC	choroid plexus:	n/a	n/a
48	POLR2A	chr11:10323855-10329868	Hela-S3	cervix:	n/a	n/a
49	YY1	chr11:10327309-10328093	HepG2	liver:	n/a	n/a
50	POLR2A	chr11:10320694-10332551	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:9777333..9782154-chr11:10324598..10331360,10	MCF-7	breast:
2	chr11:8932589..8934691-chr11:10326254..10327939,2	MCF-7	breast:
3	chr11:10075330..10076970-chr11:10327366..10329414,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254554	TF binding region
AMPD3	TF binding region
ENSG00000245522	Chromatin interaction
ENSG00000246273	Chromatin interaction
ENSG00000166452	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10128609	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10128701	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042631	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs11042649	0.84[YRI][hapmap]
rs11042651	0.93[YRI][hapmap];1.00[AMR][1000 genomes]
rs11042672	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042674	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042684	0.83[AMR][1000 genomes]
rs11042691	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042693	0.85[YRI][hapmap]
rs11042694	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042696	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042697	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042698	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042705	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042706	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042707	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042708	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042709	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042710	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042711	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11042715	1.00[EUR][1000 genomes]
rs11042722	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12269976	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12270074	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12270278	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12270822	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12271159	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12271480	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12272306	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12272934	0.85[YRI][hapmap]
rs12273035	0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12274021	0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12277936	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12279727	0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12279936	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12282728	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12285084	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12285093	0.83[AMR][1000 genomes]
rs12287964	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12288716	1.00[AMR][1000 genomes]
rs12288833	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12291188	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12291783	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12292901	0.93[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12294052	1.00[EUR][1000 genomes]
rs12294064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1372812	0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1372813	0.80[YRI][hapmap]
rs16907586	0.82[YRI][hapmap]
rs16907612	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16907632	0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4537746	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55919524	1.00[EUR][1000 genomes]
rs56948226	1.00[EUR][1000 genomes]
rs57138875	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57672320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57743646	0.83[AMR][1000 genomes]
rs58354844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59629505	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59651099	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59709366	1.00[EUR][1000 genomes]
rs59928017	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60051250	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60433518	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7942109	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10323200-10329800	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr11:10323200-10330200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr11:10323600-10330000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr11:10323800-10329000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr11:10323800-10329600	Active TSS	Placenta Amnion	Placenta Amnion
6	chr11:10323800-10330000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr11:10323800-10330000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
8	chr11:10323800-10330200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr11:10324000-10328200	Active TSS	Sigmoid Colon	Sigmoid Colon
10	chr11:10324000-10328600	Flanking Bivalent TSS/Enh	Dnd41	blood
11	chr11:10324000-10329200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr11:10324000-10329800	Active TSS	Aorta	Aorta
13	chr11:10324000-10330000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
14	chr11:10324000-10330000	Active TSS	Psoas Muscle	Psoas
15	chr11:10324000-10330200	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr11:10324200-10328000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:10324200-10328000	Active TSS	Small Intestine	intestine
18	chr11:10324200-10329800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr11:10324200-10329800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr11:10324200-10329800	Active TSS	Gastric	stomach
21	chr11:10324400-10327600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
22	chr11:10324400-10329800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:10324600-10329800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr11:10324800-10328600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
25	chr11:10324800-10328600	Flanking Bivalent TSS/Enh	Thymus	Thymus
26	chr11:10324800-10330000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
27	chr11:10325200-10329000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:10325400-10329800	Active TSS	HSMMtube	muscle
29	chr11:10325600-10328400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
30	chr11:10325600-10330000	Active TSS	Right Atrium	heart
31	chr11:10325800-10327600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr11:10325800-10327600	Active TSS	Left Ventricle	heart
33	chr11:10325800-10328000	Active TSS	HMEC	breast
34	chr11:10325800-10328200	Active TSS	HSMM	muscle
35	chr11:10325800-10328400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
36	chr11:10325800-10328400	Active TSS	Brain Substantia Nigra	brain
37	chr11:10326000-10327600	Active TSS	Hela-S3	cervix
38	chr11:10326000-10328000	Active TSS	Colon Smooth Muscle	Colon
39	chr11:10326000-10328200	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr11:10326000-10328200	Active TSS	NHEK	skin
41	chr11:10326000-10328600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
42	chr11:10326000-10330000	Active TSS	Ovary	ovary
43	chr11:10326200-10328200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr11:10326200-10328600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
45	chr11:10326200-10329800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:10326400-10327600	Active TSS	Lung	lung
47	chr11:10326400-10328600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
48	chr11:10326600-10327800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
49	chr11:10326600-10328000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
50	chr11:10326600-10328400	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links