Variant report

Variant	rs11042574
Chromosome Location	chr11:9994795-9994796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr11:9994316-9994959	HCT-116	colon:	n/a	n/a
2	RAD21	chr11:9994375-9994884	SK-N-SH_RA	brain:	n/a	n/a
3	RAD21	chr11:9994233-9995478	SK-N-SH	brain:	n/a	chr11:9995207-9995217
4	RAD21	chr11:9994403-9994848	IMR90	lung:	n/a	n/a
5	RAD21	chr11:9994489-9994901	MCF-7	breast:	n/a	n/a
6	RAD21	chr11:9994238-9995005	A549	lung:	n/a	n/a
7	CTCF	chr11:9994218-9995087	A549	lung:	n/a	n/a
8	RAD21	chr11:9994291-9994886	MCF-7	breast:	n/a	n/a
9	CTCF	chr11:9994383-9994860	A549	lung:	n/a	n/a
10	SMC3	chr11:9994423-9994835	Hela-S3	cervix:	n/a	n/a
11	SMC3	chr11:9994446-9994834	HepG2	liver:	n/a	n/a
12	CTCF	chr11:9994412-9994797	A549	lung:	n/a	n/a
13	RAD21	chr11:9994421-9994847	HepG2	liver:	n/a	n/a
14	RAD21	chr11:9994424-9994811	HepG2	liver:	n/a	n/a
15	RAD21	chr11:9994468-9994878	H1-hESC	embryonic stem cell:	n/a	n/a
16	RAD21	chr11:9994422-9994835	GM12878	blood:	n/a	n/a
17	RFX5	chr11:9994450-9994802	Hela-S3	cervix:	n/a	n/a
18	SMC3	chr11:9994401-9994915	GM12878	blood:	n/a	n/a
19	RAD21	chr11:9994443-9994806	A549	lung:	n/a	n/a
20	ZNF143	chr11:9994441-9994800	GM12878	blood:	n/a	n/a
21	CTCF	chr11:9994481-9994798	T-47D	breast:	n/a	n/a
22	RAD21	chr11:9994290-9994921	A549	lung:	n/a	n/a
23	CTCF	chr11:9994486-9994836	K562	blood:	n/a	n/a
24	RAD21	chr11:9994427-9994850	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr11:9994464-9994891	MCF-7	breast:	n/a	n/a
26	CTCF	chr11:9994466-9994900	MCF-7	breast:	n/a	n/a
27	CTCF	chr11:9994243-9995000	HCT-116	colon:	n/a	n/a
28	RUNX3	chr11:9994481-9994839	GM12878	blood:	n/a	n/a
29	RAD21	chr11:9994420-9994805	GM12878	blood:	n/a	n/a
30	RAD21	chr11:9994408-9994868	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr11:9994537-9994801	HUVEC	blood vessel:	n/a	n/a
32	TCF12	chr11:9994396-9995432	A549	lung:	n/a	n/a
33	RAD21	chr11:9994308-9994997	HCT-116	colon:	n/a	n/a
34	RAD21	chr11:9994258-9994854	HepG2	liver:	n/a	n/a
35	CTCF	chr11:9994413-9994824	IMR90	lung:	n/a	n/a
36	REST	chr11:9994473-9995085	A549	lung:	n/a	n/a
37	CTCF	chr11:9994382-9994830	HepG2	liver:	n/a	n/a
38	SMC3	chr11:9994048-9996188	SK-N-SH	brain:	n/a	n/a
39	SMC3	chr11:9994504-9994797	K562	blood:	n/a	n/a
40	RAD21	chr11:9994353-9994857	ECC-1	luminal epithelium:	n/a	n/a
41	RAD21	chr11:9994313-9994866	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr11:9994760-9994910	HepG2	liver:	n/a	n/a
43	CTCF	chr11:9994700-9994850	GM12866	blood:	n/a	n/a
44	CTCF	chr11:9994417-9994826	GM12878	blood:	n/a	n/a
45	CTCF	chr11:9994262-9995096	SK-N-SH	brain:	n/a	n/a
46	RAD21	chr11:9994382-9994840	ECC-1	luminal epithelium:	n/a	n/a
47	BRCA1	chr11:9994495-9994970	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr11:9994365-9994841	HUVEC	blood vessel:	n/a	n/a
49	CTCF	chr11:9994415-9994839	K562	blood:	n/a	n/a
50	CTCF	chr11:9994435-9994806	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:9883445..9884416-chr11:9994096..9994928,3	MCF-7	breast:
2	chr11:9883380..9884276-chr11:9994232..9995105,4	MCF-7	breast:
3	chr11:9779414..9780281-chr11:9994114..9995162,4	K562	blood:

No data

Variant related genes	Relation type
SBF2	TF binding region
ENSG00000246273	Chromatin interaction
ENSG00000245522	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10500715	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10500717	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs10743123	0.85[ASN][1000 genomes]
rs10770077	0.89[ASN][1000 genomes]
rs10770078	0.91[ASN][1000 genomes]
rs10770079	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10840330	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10840333	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10840334	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10840347	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs10840348	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs10840361	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10840362	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10840370	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs11042558	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042589	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11042590	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11042591	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11042592	0.84[AMR][1000 genomes]
rs11042604	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11042605	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11042613	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs11042624	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs11042639	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs11042645	1.00[JPT][hapmap]
rs11526057	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12221716	0.84[AMR][1000 genomes]
rs12222953	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12283105	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12290996	0.91[ASN][1000 genomes]
rs12575719	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1372807	0.88[JPT][hapmap]
rs1442732	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs16907368	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs16907396	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs2403226	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2403227	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2403229	0.81[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs4576815	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4625455	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs4909917	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4910086	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs57420335	0.88[AMR][1000 genomes]
rs58084362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60362241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106914	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7114044	0.89[ASN][1000 genomes]
rs7114303	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7933475	0.90[ASN][1000 genomes]
rs7938788	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7946995	0.94[JPT][hapmap]
rs7951950	0.88[ASN][1000 genomes]

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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv896988	chr11:9912052-10012511	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv896989	chr11:9951968-10059623	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv1819684	chr11:9973062-10012511	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9952800-9995200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:9973800-10010600	Weak transcription	Fetal Brain Male	brain
3	chr11:9974200-9994800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr11:9974200-9999000	Weak transcription	Fetal Heart	heart
5	chr11:9974200-9999000	Weak transcription	HSMMtube	muscle
6	chr11:9979400-9995000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:9979800-9999200	Weak transcription	NH-A	brain
8	chr11:9981000-10020000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:9981200-9995000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr11:9981200-10004200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:9981200-10009200	Weak transcription	Brain Germinal Matrix	brain
12	chr11:9981400-9994800	Weak transcription	Brain Hippocampus Middle	brain
13	chr11:9981400-9995200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:9981400-9995200	Weak transcription	Brain Angular Gyrus	brain
15	chr11:9981400-9995400	Weak transcription	Right Ventricle	heart
16	chr11:9981400-9999000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr11:9981400-10002200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:9981400-10003400	Weak transcription	Brain Anterior Caudate	brain
19	chr11:9981400-10003400	Weak transcription	NHEK	skin
20	chr11:9981400-10003600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr11:9981400-10004200	Weak transcription	Esophagus	oesophagus
22	chr11:9981400-10004200	Weak transcription	Lung	lung
23	chr11:9981400-10004400	Weak transcription	HepG2	liver
24	chr11:9981400-10008800	Weak transcription	Primary T cells from cord blood	blood
25	chr11:9981400-10010200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:9981400-10014800	Weak transcription	Dnd41	blood
27	chr11:9981400-10017000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr11:9981400-10051600	Weak transcription	Aorta	Aorta
29	chr11:9981600-10003400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr11:9981800-9995200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:9981800-10003400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr11:9981800-10004800	Weak transcription	Ovary	ovary
33	chr11:9983600-10004800	Weak transcription	Fetal Lung	lung
34	chr11:9983600-10023200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:9983800-9997200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr11:9984600-10010200	Weak transcription	Fetal Kidney	kidney
37	chr11:9984800-9999200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:9985000-9998000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:9985800-9995000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr11:9985800-9997600	Weak transcription	Fetal Intestine Small	intestine
41	chr11:9985800-9998800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr11:9985800-10000600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:9985800-10004000	Weak transcription	Placenta	Placenta
44	chr11:9985800-10004200	Weak transcription	Fetal Muscle Leg	muscle
45	chr11:9985800-10004400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr11:9985800-10021600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:9985800-10023600	Weak transcription	Primary B cells from cord blood	blood
48	chr11:9985800-10049000	Weak transcription	Left Ventricle	heart
49	chr11:9986000-10006000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:9987200-10003600	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links