Variant report

Variant	rs11264426
Chromosome Location	chr1:155940948-155940949
allele	G/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:5)
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	NFIC	chr1:155940216-155941126	GM12878	blood:	n/a	n/a
2	TEAD4	chr1:155939902-155941068	K562	blood:	n/a	n/a
3	RCOR1	chr1:155940271-155940952	K562	blood:	n/a	n/a
4	POLR2A	chr1:155938318-155941155	U87	brain:	n/a	n/a
5	ELF1	chr1:155940280-155941032	K562	blood:	n/a	n/a
6	RCOR1	chr1:155940297-155941022	K562	blood:	n/a	n/a
7	STAT5A	chr1:155940178-155941102	GM12878	blood:	n/a	n/a
8	PML	chr1:155940018-155941071	K562	blood:	n/a	n/a
9	MTA3	chr1:155939979-155941076	GM12878	blood:	n/a	n/a
10	RUNX3	chr1:155940241-155941054	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:155940261-155940965	GM12891	blood:	n/a	n/a
12	WRNIP1	chr1:155940051-155941045	GM12878	blood:	n/a	n/a
13	MAX	chr1:155940759-155941002	K562	blood:	n/a	n/a
14	RCOR1	chr1:155939706-155941136	IMR90	lung:	n/a	n/a
15	MXI1	chr1:155938924-155941109	IMR90	lung:	n/a	n/a
16	EGR1	chr1:155940674-155941041	K562	blood:	n/a	chr1:155940874-155940888 chr1:155940848-155940862
17	MYC	chr1:155940238-155941033	NB4	blood:	n/a	n/a
18	RUNX3	chr1:155940148-155941139	GM12878	blood:	n/a	n/a
19	ELF1	chr1:155940210-155940957	GM12878	blood:	n/a	n/a
20	MAZ	chr1:155940396-155940982	GM12878	blood:	n/a	n/a
21	E2F6	chr1:155940826-155941006	K562	blood:	n/a	n/a
22	MAZ	chr1:155939849-155941074	IMR90	lung:	n/a	n/a
23	SPI1	chr1:155939915-155941109	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:155940197-155941034	GM12891	blood:	n/a	n/a
25	JUN	chr1:155939954-155941154	K562	blood:	n/a	n/a
26	ELF1	chr1:155940329-155941086	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:155938324-155941149	U87	brain:	n/a	n/a
28	MAX	chr1:155940243-155941025	NB4	blood:	n/a	n/a
29	TBL1XR1	chr1:155940942-155940979	K562	blood:	n/a	n/a
30	POLR2A	chr1:155940069-155941077	GM12892	blood:	n/a	n/a
31	POLR2A	chr1:155938368-155941160	HL-60	blood:	n/a	n/a
32	ZC3H11A	chr1:155940919-155940966	K562	blood:	n/a	n/a
33	ZNF263	chr1:155940480-155941043	HEK293-T-REx	kidney:	n/a	chr1:155940785-155940806 chr1:155940816-155940837 chr1:155940757-155940778
34	SPI1	chr1:155940133-155941074	HL-60	blood:	n/a	n/a
35	POLR2A	chr1:155940680-155940956	GM12878	blood:	n/a	n/a
36	UBTF	chr1:155940271-155941008	K562	blood:	n/a	n/a
37	POLR2A	chr1:155938465-155941034	K562	blood:	n/a	n/a
38	IKZF1	chr1:155940368-155941012	GM12878	blood:	n/a	n/a
39	REST	chr1:155940775-155940990	K562	blood:	n/a	n/a
40	PML	chr1:155940112-155941063	GM12878	blood:	n/a	n/a
41	CHD1	chr1:155940722-155940969	GM12878	blood:	n/a	n/a
42	MAX	chr1:155940255-155941051	K562	blood:	n/a	n/a
43	EP300	chr1:155940314-155940999	K562	blood:	n/a	n/a
44	POLR2A	chr1:155940063-155941028	U87	brain:	n/a	n/a
45	EGR1	chr1:155940741-155941018	K562	blood:	n/a	chr1:155940874-155940888 chr1:155940848-155940862
46	POLR2A	chr1:155939728-155941133	HL-60	blood:	n/a	n/a
47	MAZ	chr1:155940295-155941014	K562	blood:	n/a	n/a
48	NR2F2	chr1:155940010-155941011	K562	blood:	n/a	n/a
49	CBX3	chr1:155940199-155941088	K562	blood:	n/a	n/a
50	CHD2	chr1:155940300-155941015	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155932456..155935172-chr1:155940207..155941869,2	MCF-7	breast:
2	chr1:155902827..155906202-chr1:155937016..155941458,5	MCF-7	breast:
3	chr1:155910039..155911830-chr1:155939353..155941637,2	K562	blood:
4	chr1:155902972..155905635-chr1:155940527..155942498,2	K562	blood:
5	chr1:155902826..155904472-chr1:155940527..155942381,2	K562	blood:

No data

Variant related genes	Relation type
ARHGEF2	TF binding region
ENSG00000116584	Chromatin interaction
ENSG00000132680	Chromatin interaction
ENSG00000173080	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10796955	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1111102	0.86[CEU][hapmap]
rs11585845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12037177	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs12080846	0.93[ASN][1000 genomes]
rs12091273	0.93[ASN][1000 genomes]
rs12091361	0.93[ASN][1000 genomes]
rs12118795	0.90[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs12568523	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1889532	1.00[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1889533	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2016251	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.92[ASN][1000 genomes]
rs2282301	0.95[CEU][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs2297649	0.95[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2364403	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[ASN][1000 genomes]
rs4661217	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4661218	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61813286	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6427297	0.81[CEU][hapmap]
rs6667652	0.95[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs6670493	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6696019	0.95[CEU][hapmap];0.86[JPT][hapmap]
rs729022	0.82[MEX][hapmap]
rs7534858	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs867549	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs867550	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs915178	0.86[CEU][hapmap]
rs915181	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.92[ASN][1000 genomes]
rs928596	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.96[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	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11264426	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs11264426	RIT1	cis	cerebellum	SCAN
rs11264426	YY1AP1	cis	cerebellum	SCAN
rs11264426	SPRR3	cis	parietal	SCAN
rs11264426	RIT1	cis	Thyroid	GTEx
rs11264426	ROBLD3	cis	parietal	SCAN
rs11264426	PRUNE	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155905000-155945600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:155933000-155942200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:155934800-155944400	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr1:155935000-155942800	Genic enhancers	Right Ventricle	heart
5	chr1:155935000-155943200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:155935000-155944800	Enhancers	Fetal Heart	heart
7	chr1:155935200-155941000	Genic enhancers	Lung	lung
8	chr1:155936200-155941000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:155936200-155941400	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:155936400-155941000	Genic enhancers	Gastric	stomach
11	chr1:155936400-155944000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:155936600-155941000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:155936600-155941000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:155936600-155941200	Flanking Active TSS	Brain Anterior Caudate	brain
15	chr1:155936600-155944200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:155936800-155941000	Enhancers	Right Atrium	heart
17	chr1:155936800-155944600	Genic enhancers	Fetal Stomach	stomach
18	chr1:155937000-155941200	Enhancers	Liver	Liver
19	chr1:155937000-155944200	Genic enhancers	Thymus	Thymus
20	chr1:155937200-155941000	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr1:155937200-155941000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:155937600-155941000	Enhancers	Left Ventricle	heart
23	chr1:155937600-155942600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:155937800-155941000	Strong transcription	Hela-S3	cervix
25	chr1:155937800-155942800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr1:155938000-155941000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:155938000-155942200	Genic enhancers	Primary T cells fromperipheralblood	blood
28	chr1:155938000-155944400	Genic enhancers	Fetal Thymus	thymus
29	chr1:155938200-155943200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:155938200-155944000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
31	chr1:155938400-155942800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr1:155938800-155941000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr1:155938800-155941200	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr1:155938800-155941800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:155939000-155941200	Enhancers	H1 Cell Line	embryonic stem cell
36	chr1:155939000-155941200	Enhancers	Fetal Brain Male	brain
37	chr1:155939000-155942200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
38	chr1:155939200-155941000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:155939200-155943600	Weak transcription	Fetal Kidney	kidney
40	chr1:155939400-155941000	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr1:155939400-155944000	Genic enhancers	Fetal Muscle Leg	muscle
42	chr1:155939600-155941000	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr1:155939600-155942000	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr1:155939600-155942600	Enhancers	Small Intestine	intestine
45	chr1:155939800-155941000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:155939800-155941000	Enhancers	Esophagus	oesophagus
47	chr1:155939800-155941000	Enhancers	Pancreas	Pancrea
48	chr1:155939800-155941000	Genic enhancers	Stomach Mucosa	stomach
49	chr1:155939800-155941200	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr1:155939800-155941600	Flanking Active TSS	GM12878-XiMat	blood

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