Variant report

Variant	rs3809060
Chromosome Location	chr11:32458807-32458808
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:32458391-32461056	H1-neurons	neurons:	n/a	n/a
2	SUZ12	chr11:32453725-32461544	NT2-D1	testis:	n/a	n/a
3	CTBP2	chr11:32457051-32458830	H1-hESC	embryonic stem cell:	n/a	n/a
4	SUZ12	chr11:32453771-32458890	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr11:32458208-32461069	H1-neurons	neurons:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:32458769-32458819	GM12878	blood:	n/a
2	chr11:32458769-32458819	HPAEpiC	pulmonary alveolar:	n/a
3	chr11:32458769-32458819	MCF-7	breast:	n/a
4	chr11:32458769-32458819	PrEC	prostate:	n/a
5	chr11:32458769-32458819	HepG2	liver:	n/a
6	chr11:32458769-32458819	NB4	blood:	n/a
7	chr11:32458769-32458819	HAEpiC	amniotic membrane:	n/a
8	chr11:32458769-32458819	HCPEpiC	choroid plexus:	n/a
9	chr11:32458769-32458819	AG10803	skin:	n/a
10	chr11:32458769-32458819	HCF	heart:	n/a
11	chr11:32458769-32458819	GM12892	blood:	n/a
12	chr11:32458769-32458819	ProgFib	skin:	n/a
13	chr11:32458769-32458819	SKMC	muscle:	n/a
14	chr11:32458769-32458819	HL-60	blood:	n/a
15	chr11:32458769-32458819	BE2_C	brain:	n/a
16	chr11:32458769-32458819	A549	lung:	n/a
17	chr11:32458769-32458819	HEEpiC	esophagus:	n/a
18	chr11:32458769-32458819	LNCaP	prostate:	n/a
19	chr11:32458769-32458819	ECC-1	luminal epithelium:	n/a
20	chr11:32458769-32458819	AoSMC	blood vessel:	n/a
21	chr11:32458769-32458819	IMR90	lung:	fetal
22	chr11:32458769-32458819	SK-N-MC	brain:	n/a
23	chr11:32458769-32458819	HRPEpiC	eye:	n/a
24	chr11:32458769-32458819	NH-A	brain:	n/a
25	chr11:32458769-32458819	HRE	kidney:	n/a
26	chr11:32458769-32458819	HIPEpiC	eye:	n/a
27	chr11:32458769-32458819	AG04449	skin:	fetal
28	chr11:32458769-32458819	AG09309	skin:	n/a
29	chr11:32458769-32458819	PFSK-1	brain:	n/a
30	chr11:32458769-32458819	NHDF-neo	bronchial:	n/a
31	chr11:32458769-32458819	HMEC	breast:	n/a
32	chr11:32458769-32458819	U87	brain:	n/a
33	chr11:32458769-32458819	GM12891	blood:	n/a
34	chr11:32458769-32458819	NHBE	bronchial:	n/a
35	chr11:32458769-32458819	HRCEpiC	kidney:	n/a
36	chr11:32458769-32458819	Hepatocyte	liver:	n/a
37	chr11:32458769-32458819	K562	blood:	n/a
38	chr11:32458769-32458819	SAEC	small airway:	n/a
39	chr11:32458769-32458819	AG04450	lung:	fetal
40	chr11:32458769-32458819	GM19239	blood:	n/a
41	chr11:32458769-32458819	Jurkat	blood:	n/a
42	chr11:32458769-32458819	Hela-S3	cervix:	n/a
43	chr11:32458769-32458819	HNPCEpiC	eye:	n/a
44	chr11:32458769-32458819	AG09319	gingival:	n/a
45	chr11:32458769-32458819	SK-N-SH	brain:	n/a
46	chr11:32458769-32458819	MCF10A-Er-Src	breast:	n/a
47	chr11:32458769-32458819	GM06990	blood:	n/a
48	chr11:32458769-32458819	CMK	blood:	n/a
49	chr11:32458769-32458819	Caco-2	colon:	n/a
50	chr11:32458769-32458819	RPTEC	kidney:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:32455134..32460391-chr11:32603988..32611641,10	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EIF3M-2	chr11:32457585-32460136	NONHSAT018664

No data

Variant related genes	Relation type
WT1	TF binding region
WT1-AS	TF binding region
WT1-AS	CpG island
WT1	CpG island
ENSG00000149100	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10742277	0.95[CEU][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10835917	0.82[CHD][hapmap];0.80[TSI][hapmap]
rs11031783	0.92[ASN][1000 genomes]
rs11031784	0.92[ASN][1000 genomes]
rs2234580	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2234585	0.81[ASN][1000 genomes]
rs2301250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2301251	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2301252	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2301253	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2301254	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3809061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809062	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858445	0.81[CHD][hapmap]
rs3858446	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3858447	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3858448	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3858449	0.81[CHD][hapmap]
rs3858454	0.92[CHD][hapmap];0.81[GIH][hapmap]
rs3886325	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4140413	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5030141	0.81[CHD][hapmap]
rs5030171	0.81[ASN][1000 genomes]
rs5030176	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5030178	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5030179	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7110547	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7120686	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7126322	0.80[ASN][1000 genomes]
rs7946086	0.81[CEU][hapmap];0.89[GIH][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	nsv832108	chr11:32395937-32560583	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1044547	chr11:32435753-32465233	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2753303	chr11:32447324-32494924	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1051559	chr11:32447347-32465233	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3809060	WT1AS	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:32453400-32459600	Active TSS	Right Atrium	heart
2	chr11:32454600-32459800	Active TSS	Ovary	ovary
3	chr11:32455000-32459400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
4	chr11:32455800-32459000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr11:32456400-32459000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
6	chr11:32456800-32459600	Active TSS	Right Ventricle	heart
7	chr11:32456800-32460400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
8	chr11:32457000-32462600	Bivalent/Poised TSS	Fetal Kidney	kidney
9	chr11:32457200-32460600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:32457200-32461000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr11:32457400-32459400	Bivalent Enhancer	Brain Germinal Matrix	brain
12	chr11:32457400-32460000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr11:32457600-32459400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:32457600-32460800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr11:32457800-32459000	Bivalent/Poised TSS	Primary T cells from cord blood	blood
16	chr11:32458000-32459000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
17	chr11:32458000-32459000	Bivalent Enhancer	Liver	Liver
18	chr11:32458000-32459400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:32458000-32459400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:32458000-32459400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:32458000-32459400	Enhancers	Spleen	Spleen
22	chr11:32458000-32460600	Bivalent Enhancer	Fetal Muscle Leg	muscle
23	chr11:32458200-32459000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
24	chr11:32458200-32459400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr11:32458200-32459400	Bivalent Enhancer	Fetal Thymus	thymus
26	chr11:32458200-32459800	Bivalent Enhancer	Fetal Stomach	stomach
27	chr11:32458200-32460400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
28	chr11:32458200-32460600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
29	chr11:32458400-32459200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
30	chr11:32458600-32459000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
31	chr11:32458600-32459000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr11:32458600-32459400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
33	chr11:32458600-32459600	Weak transcription	Gastric	stomach
34	chr11:32458600-32461200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
35	chr11:32458600-32461200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
36	chr11:32458800-32459000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr11:32458800-32459000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
38	chr11:32458800-32459000	Bivalent Enhancer	Placenta	Placenta
39	chr11:32458800-32460400	Weak transcription	Pancreas	Pancrea

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