Variant report

Variant	rs11202878
Chromosome Location	chr10:90640971-90640972
allele	A/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	ZBTB7A	chr10:90640390-90640988	ECC-1	luminal epithelium:	n/a	n/a
2	TAF1	chr10:90639558-90641029	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr10:90639586-90641828	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr10:90639480-90641613	U87	brain:	n/a	n/a
5	POLR2A	chr10:90639409-90641040	GM12892	blood:	n/a	n/a
6	MAX	chr10:90639494-90640977	A549	lung:	n/a	chr10:90640816-90640826
7	POLR2A	chr10:90639531-90641494	GM18951	blood:	n/a	n/a
8	MXI1	chr10:90639555-90641039	GM12878	blood:	n/a	n/a
9	POLR2A	chr10:90640037-90641039	MCF10A-Er-Src	breast:	n/a	n/a
10	WRNIP1	chr10:90639531-90640975	GM12878	blood:	n/a	n/a
11	RAD21	chr10:90639665-90640999	ECC-1	luminal epithelium:	n/a	chr10:90640670-90640684
12	POLR2A	chr10:90639563-90641024	GM12891	blood:	n/a	n/a
13	TCF12	chr10:90639595-90641139	A549	lung:	n/a	n/a
14	POLR2A	chr10:90639293-90641628	GM12892	blood:	n/a	n/a
15	POLR2A	chr10:90639521-90641000	HL-60	blood:	n/a	n/a
16	POLR2A	chr10:90639591-90641016	GM12891	blood:	n/a	n/a
17	BCLAF1	chr10:90639559-90641144	GM12878	blood:	n/a	chr10:90639918-90639927 chr10:90639921-90639930 chr10:90639918-90639931
18	POLR2A	chr10:90639363-90641045	HL-60	blood:	n/a	n/a
19	ZNF384	chr10:90640351-90641353	GM12878	blood:	n/a	n/a
20	POLR2A	chr10:90639519-90641333	GM15510	blood:	n/a	n/a
21	POLR2A	chr10:90639558-90641614	U87	brain:	n/a	n/a
22	RELA	chr10:90639550-90641028	GM19099	blood:	n/a	n/a
23	POLR2A	chr10:90639689-90641264	MCF10A-Er-Src	breast:	n/a	n/a
24	MYC	chr10:90639569-90641297	Hela-S3	cervix:	n/a	chr10:90640816-90640826
25	EP300	chr10:90639535-90641084	SK-N-SH	brain:	n/a	chr10:90639920-90639929 chr10:90640598-90640607 chr10:90639917-90639926
26	POLR2A	chr10:90639404-90641662	GM12878	blood:	n/a	n/a
27	POLR2A	chr10:90639683-90641292	GM10847	blood:	n/a	n/a
28	POLR2A	chr10:90639871-90641559	IMR90	lung:	n/a	n/a
29	BRCA1	chr10:90640108-90641607	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr10:90639325-90641716	PANC-1	pancreas:	n/a	n/a
31	MAX	chr10:90639617-90641007	ECC-1	luminal epithelium:	n/a	chr10:90640816-90640826
32	STAT1	chr10:90639559-90641728	Hela-S3	cervix:	n/a	chr10:90640658-90640666 chr10:90641185-90641194 chr10:90641186-90641195 chr10:90641183-90641197 chr10:90641180-90641200
33	REST	chr10:90639496-90641065	A549	lung:	n/a	n/a
34	TCF12	chr10:90639777-90640994	GM12878	blood:	n/a	n/a
35	EP300	chr10:90638590-90642773	SK-N-SH	brain:	n/a	chr10:90639920-90639929 chr10:90638982-90638996 chr10:90640598-90640607 chr10:90639917-90639926
36	MAX	chr10:90639598-90641109	ECC-1	luminal epithelium:	n/a	chr10:90640816-90640826
37	POLR2A	chr10:90639559-90640972	GM12891	blood:	n/a	n/a
38	POLR2A	chr10:90639271-90640980	GM12878	blood:	n/a	n/a
39	POLR2A	chr10:90639582-90641376	Raji	blood:	n/a	n/a
40	EGR1	chr10:90639466-90641004	HCT-116	colon:	n/a	chr10:90640406-90640415
41	RELA	chr10:90639374-90641448	GM18505	blood:	n/a	n/a
42	TAF1	chr10:90639625-90641137	A549	lung:	n/a	n/a
43	POLR2A	chr10:90639019-90642990	Hela-S3	cervix:	n/a	n/a
44	CHD1	chr10:90639393-90641444	GM12878	blood:	n/a	n/a
45	SP1	chr10:90639451-90641003	A549	lung:	n/a	chr10:90640815-90640827 chr10:90640812-90640826 chr10:90640808-90640822 chr10:90639546-90639560 chr10:90639871-90639885 chr10:90640815-90640827
46	MAZ	chr10:90639480-90641350	GM12878	blood:	n/a	chr10:90640816-90640826
47	STAT5A	chr10:90639438-90641295	GM12878	blood:	n/a	chr10:90640658-90640666 chr10:90641185-90641194 chr10:90641186-90641195 chr10:90641183-90641197 chr10:90641180-90641200
48	MXI1	chr10:90638998-90642809	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr10:90639244-90642743	U87	brain:	n/a	n/a
50	TCF12	chr10:90639425-90641719	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:90640525..90641354-chr3:152880444..152881083,2	Hela-S3	cervix:
2	chr10:90640938..90641679-chr20:47537836..47538414,2	Hela-S3	cervix:
3	chr10:90639301..90642051-chr10:90749823..90751899,2	MCF-7	breast:
4	chr10:90640395..90641243-chr19:1269206..1269798,2	Hela-S3	cervix:

Variant related genes	Relation type
STAMBPL1	TF binding region
ENSG00000026103	Chromatin interaction
ENSG00000099622	Chromatin interaction
ENSG00000107796	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11202877	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11202880	0.81[AFR][1000 genomes]
rs12248501	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12262249	0.83[AFR][1000 genomes]
rs12264141	0.83[AFR][1000 genomes]
rs12269097	0.82[AFR][1000 genomes]
rs1441742	0.81[ASN][1000 genomes]
rs1926184	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1926185	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1926186	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55885377	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57063754	0.83[AFR][1000 genomes]
rs57261011	0.85[AMR][1000 genomes]
rs7075596	1.00[EUR][1000 genomes]
rs74150105	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs755049	1.00[EUR][1000 genomes]
rs7910708	0.82[AFR][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	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active 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 miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90639000-90642200	Active TSS	Rectal Smooth Muscle	rectum
2	chr10:90639200-90641200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr10:90639200-90642000	Active TSS	Brain Cingulate Gyrus	brain
4	chr10:90639200-90642000	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr10:90639200-90642400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:90639400-90641000	Active TSS	NH-A	brain
7	chr10:90639400-90641200	Active TSS	H1 Cell Line	embryonic stem cell
8	chr10:90639400-90641200	Active TSS	H9 Cell Line	embryonic stem cell
9	chr10:90639400-90641200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr10:90639400-90641200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr10:90639400-90641200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr10:90639400-90641200	Active TSS	HSMM	muscle
13	chr10:90639400-90641400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr10:90639400-90641400	Active TSS	Brain Angular Gyrus	brain
15	chr10:90639400-90641400	Active TSS	Brain Substantia Nigra	brain
16	chr10:90639400-90641400	Active TSS	HSMMtube	muscle
17	chr10:90639400-90641800	Active TSS	Ovary	ovary
18	chr10:90639400-90642000	Active TSS	Right Atrium	heart
19	chr10:90639400-90642400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr10:90639600-90641000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:90639600-90641000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr10:90639600-90641000	Active TSS	Esophagus	oesophagus
23	chr10:90639600-90641000	Active TSS	Gastric	stomach
24	chr10:90639600-90641000	Active TSS	Pancreas	Pancrea
25	chr10:90639600-90641000	Active TSS	Small Intestine	intestine
26	chr10:90639600-90641000	Active TSS	Spleen	Spleen
27	chr10:90639600-90641200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr10:90639600-90641200	Active TSS	Left Ventricle	heart
29	chr10:90639600-90641400	Active TSS	Right Ventricle	heart
30	chr10:90639600-90641600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr10:90639600-90641600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr10:90639600-90641600	Active TSS	Colonic Mucosa	Colon
33	chr10:90639600-90641600	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr10:90639600-90641800	Active TSS	Colon Smooth Muscle	Colon
35	chr10:90639600-90643000	Active TSS	A549	lung
36	chr10:90639800-90641000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr10:90639800-90641000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr10:90639800-90641000	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr10:90639800-90641000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr10:90639800-90641000	Active TSS	Muscle Satellite Cultured Cells	--
41	chr10:90639800-90641000	Active TSS	Fetal Kidney	kidney
42	chr10:90639800-90641200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr10:90639800-90641200	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr10:90639800-90641200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr10:90639800-90641200	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr10:90639800-90641200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr10:90639800-90641200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr10:90639800-90641200	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr10:90639800-90641200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:90639800-90641200	Active TSS	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links