Variant report

Variant	rs1300845
Chromosome Location	chr11:64819168-64819169
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr11:64818461-64819355	GM12878	blood:	n/a	n/a
2	ATF2	chr11:64818853-64819348	GM12878	blood:	n/a	n/a
3	TCF12	chr11:64819044-64819225	GM12878	blood:	n/a	n/a
4	CEBPB	chr11:64819117-64819459	K562	blood:	n/a	chr11:64819284-64819295
5	POLR2A	chr11:64818550-64819228	Hela-S3	cervix:	n/a	n/a
6	NFATC1	chr11:64818800-64819373	GM12878	blood:	n/a	n/a
7	SRF	chr11:64819063-64819182	GM12878	blood:	n/a	n/a
8	HEY1	chr11:64818557-64819214	K562	blood:	n/a	n/a
9	EBF1	chr11:64818954-64819367	GM12878	blood:	n/a	n/a
10	STAT5A	chr11:64818916-64819309	GM12878	blood:	n/a	n/a
11	CEBPB	chr11:64819126-64819443	HepG2	liver:	n/a	chr11:64819284-64819295
12	NFIC	chr11:64818847-64819415	GM12878	blood:	n/a	n/a
13	MAX	chr11:64818795-64819170	K562	blood:	n/a	n/a
14	BCL3	chr11:64818912-64819267	GM12878	blood:	n/a	n/a
15	MTA3	chr11:64818811-64819435	GM12878	blood:	n/a	n/a
16	BCL11A	chr11:64818967-64819329	GM12878	blood:	n/a	n/a
17	ATF2	chr11:64818826-64819392	GM12878	blood:	n/a	n/a
18	NFIC	chr11:64818822-64819303	GM12878	blood:	n/a	n/a
19	CEBPB	chr11:64819137-64819411	A549	lung:	n/a	chr11:64819284-64819295
20	PML	chr11:64818713-64819509	GM12878	blood:	n/a	n/a
21	BATF	chr11:64818932-64819262	GM12878	blood:	n/a	n/a
22	BCLAF1	chr11:64818859-64819377	GM12878	blood:	n/a	n/a
23	FOXM1	chr11:64818830-64819357	GM12878	blood:	n/a	n/a
24	POLR2A	chr11:64818524-64819205	K562	blood:	n/a	n/a
25	POLR2A	chr11:64818542-64819188	K562	blood:	n/a	n/a
26	IKZF1	chr11:64818958-64819250	GM12878	blood:	n/a	n/a
27	CEBPB	chr11:64819105-64819456	IMR90	lung:	n/a	chr11:64819284-64819295
28	MTA3	chr11:64818826-64819297	GM12878	blood:	n/a	n/a
29	RUNX3	chr11:64818538-64819365	GM12878	blood:	n/a	n/a
30	IRF4	chr11:64818901-64819378	GM12878	blood:	n/a	n/a
31	BATF	chr11:64818906-64819262	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:64819126-64819176	HCPEpiC	choroid plexus:	n/a
2	chr11:64819126-64819176	GM19239	blood:	n/a
3	chr11:64819126-64819176	MCF-7	breast:	n/a
4	chr11:64819126-64819176	GM12878	blood:	n/a
5	chr11:64819126-64819176	PrEC	prostate:	n/a
6	chr11:64819126-64819176	SK-N-SH	brain:	n/a
7	chr11:64819126-64819176	HRE	kidney:	n/a
8	chr11:64819126-64819176	SK-N-MC	brain:	n/a
9	chr11:64819126-64819176	AG04449	skin:	fetal
10	chr11:64819126-64819176	SAEC	small airway:	n/a
11	chr11:64819126-64819176	NHDF-neo	bronchial:	n/a
12	chr11:64819126-64819176	HIPEpiC	eye:	n/a
13	chr11:64819126-64819176	RPTEC	kidney:	n/a
14	chr11:64819126-64819176	U87	brain:	n/a
15	chr11:64819126-64819176	AG10803	skin:	n/a
16	chr11:64819126-64819176	NB4	blood:	n/a
17	chr11:64819126-64819176	BJ	skin:	n/a
18	chr11:64819126-64819176	AoSMC	blood vessel:	n/a
19	chr11:64819126-64819176	HRCEpiC	kidney:	n/a
20	chr11:64819126-64819176	NH-A	brain:	n/a
21	chr11:64819126-64819176	A549	lung:	n/a
22	chr11:64819126-64819176	Hela-S3	cervix:	n/a
23	chr11:64819126-64819176	K562	blood:	n/a
24	chr11:64819126-64819176	Jurkat	blood:	n/a
25	chr11:64819126-64819176	HCT-116	colon:	n/a
26	chr11:64819126-64819176	Hepatocyte	liver:	n/a
27	chr11:64819126-64819176	HCF	heart:	n/a
28	chr11:64819126-64819176	NT2-D1	testis:	n/a
29	chr11:64819126-64819176	BE2_C	brain:	n/a
30	chr11:64819126-64819176	PFSK-1	brain:	n/a
31	chr11:64819126-64819176	LNCaP	prostate:	n/a
32	chr11:64819126-64819176	ProgFib	skin:	n/a
33	chr11:64819126-64819176	HNPCEpiC	eye:	n/a
34	chr11:64819126-64819176	HepG2	liver:	n/a
35	chr11:64819126-64819176	HRPEpiC	eye:	n/a
36	chr11:64819126-64819176	PANC-1	pancreas:	n/a
37	chr11:64819126-64819176	HUVEC	blood vessel:	n/a
38	chr11:64819126-64819176	IMR90	lung:	fetal
39	chr11:64819126-64819176	ovcar-3	ovarian:	n/a
40	chr11:64819126-64819176	H1-hESC	embryonic stem cell:	embryo
41	chr11:64819126-64819176	MCF10A-Er-Src	breast:	n/a
42	chr11:64819126-64819176	AG09309	skin:	n/a
43	chr11:64819126-64819176	CMK	blood:	n/a
44	chr11:64819126-64819176	HAEpiC	amniotic membrane:	n/a
45	chr11:64819126-64819176	GM06990	blood:	n/a
46	chr11:64819126-64819176	T-47D	breast:	n/a
47	chr11:64819126-64819176	ECC-1	luminal epithelium:	n/a
48	chr11:64819126-64819176	HPAEpiC	pulmonary alveolar:	n/a
49	chr11:64819126-64819176	HEEpiC	esophagus:	n/a
50	chr11:64819126-64819176	HCM	heart:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64807871..64811209-chr11:64819025..64821229,4	MCF-7	breast:
2	chr11:64819003..64820709-chr11:64820825..64822558,3	K562	blood:
3	chr11:64817752..64820566-chr11:64835947..64837906,2	K562	blood:
4	chr11:64810649..64814377-chr11:64818779..64822031,5	K562	blood:
5	chr11:64812432..64815528-chr11:64818635..64820425,3	K562	blood:
6	chr11:64808310..64809815-chr11:64818321..64820626,2	K562	blood:
7	chr11:64789917..64792279-chr11:64818238..64820270,2	K562	blood:
8	chr11:64808319..64812889-chr11:64818537..64822434,8	MCF-7	breast:

No data

Variant related genes	Relation type
NAALADL1	TF binding region
RN7SL114P	TF binding region
NAALADL1	CpG island
RN7SL114P	CpG island
ENSG00000168060	Chromatin interaction
ENSG00000168061	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10897544	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11231929	0.85[JPT][hapmap]
rs1129195	0.83[CHB][hapmap]
rs2282499	0.83[CHB][hapmap]
rs2458298	0.94[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2507814	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3741390	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3759041	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3782094	0.89[CHB][hapmap]
rs3850946	0.83[CEU][hapmap]
rs3850947	0.83[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs476824	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs477539	0.85[JPT][hapmap]
rs486984	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs488686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs502333	0.94[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs525433	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs533018	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562590	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs566221	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613874	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs620981	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs678614	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs947799	0.80[CEU][hapmap];0.89[CHB][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	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv897709	chr11:64772545-64870779	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv897710	chr11:64772545-64885445	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv897711	chr11:64772545-64900270	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1300845	SPDYC	cis	parietal	SCAN
rs1300845	RAB1B	cis	parietal	SCAN
rs1300845	SCGB2A2	cis	cerebellum	SCAN
rs1300845	SNX15	cis	parietal	SCAN
rs1300845	MARK2	cis	cerebellum	SCAN
rs1300845	SNX15	cis	Muscle Skeletal	GTEx
rs1300845	SNX15	cis	lymphoblastoid	seeQTL
rs1300845	LRRN4CL	cis	parietal	SCAN
rs1300845	B3GAT3	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64812600-64820200	Weak transcription	HMEC	breast
2	chr11:64813400-64821200	Weak transcription	Primary T cells from cord blood	blood
3	chr11:64813400-64824200	Weak transcription	HepG2	liver
4	chr11:64813800-64833200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:64814000-64827600	Weak transcription	Pancreas	Pancrea
6	chr11:64815800-64821000	Weak transcription	Fetal Thymus	thymus
7	chr11:64816000-64820200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr11:64816000-64820800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:64816000-64820800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr11:64816000-64821000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:64816000-64821000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:64816000-64821000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr11:64816000-64821000	Weak transcription	Fetal Intestine Large	intestine
14	chr11:64816000-64821000	Weak transcription	Fetal Intestine Small	intestine
15	chr11:64816000-64821000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr11:64816000-64821200	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr11:64816000-64821200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr11:64816000-64821200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr11:64816000-64821400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr11:64816200-64820000	Weak transcription	Esophagus	oesophagus
21	chr11:64816200-64820200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr11:64816200-64820200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:64816200-64820400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:64816200-64821000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr11:64816200-64821000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr11:64816200-64821000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr11:64816200-64821000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:64816200-64825800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr11:64816400-64821400	Weak transcription	Spleen	Spleen
30	chr11:64816600-64820200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr11:64818400-64819200	Enhancers	K562	blood
32	chr11:64818400-64819400	Enhancers	GM12878-XiMat	blood
33	chr11:64818600-64819200	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr11:64818800-64819200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links