Variant report

Variant	rs535752
Chromosome Location	chr11:65828625-65828626
allele	G/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	POLR2A	chr11:65828424-65829305	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr11:65828575-65829511	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:65828601-65829520	K562	blood:	n/a	n/a
4	POLR2A	chr11:65828171-65828629	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:65828451-65828667	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65769145..65771135-chr11:65826724..65830064,3	MCF-7	breast:
2	chr11:65768235..65770195-chr11:65828585..65830132,2	MCF-7	breast:
3	chr11:65826244..65833224-chr11:65834439..65839387,11	MCF-7	breast:

Variant related genes	Relation type
SF3B2	TF binding region
ENSG00000175376	Chromatin interaction
ENSG00000175334	Chromatin interaction
ENSG00000175115	Chromatin interaction
ENSG00000255038	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1049872	0.83[EUR][1000 genomes]
rs1203998	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12803276	0.84[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs17147371	0.84[MEX][hapmap]
rs2000672	0.81[EUR][1000 genomes]
rs2452680	0.88[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2576	0.80[MEX][hapmap]
rs33988687	0.83[EUR][1000 genomes]
rs34073119	0.81[EUR][1000 genomes]
rs34123790	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35611816	0.96[EUR][1000 genomes]
rs477280	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs491618	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs503156	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs547404	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs557799	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs570887	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574153	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7480811	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs873491	0.84[MEX][hapmap]
rs947847	1.00[CEU][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
3	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
4	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
6	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs535752	SLC22A6	cis	cerebellum	SCAN
rs535752	SF3B2	cis	cerebellum	SCAN
rs535752	SF3B2	cis	parietal	SCAN
rs535752	RBM14	cis	cerebellum	SCAN
rs535752	SF3B2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65821000-65835600	Weak transcription	Right Atrium	heart
2	chr11:65821000-65836600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:65821000-65836600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:65821200-65829000	Weak transcription	Fetal Heart	heart
5	chr11:65821200-65832000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:65821200-65832200	Strong transcription	Fetal Muscle Leg	muscle
7	chr11:65821200-65835400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:65821200-65835600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:65821200-65836000	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:65821200-65836000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:65821200-65836000	Strong transcription	Fetal Intestine Large	intestine
12	chr11:65821200-65836000	Strong transcription	NHLF	lung
13	chr11:65821200-65836200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:65821200-65836600	Strong transcription	Fetal Stomach	stomach
15	chr11:65821400-65830400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:65821400-65831400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:65821400-65831800	Strong transcription	Fetal Intestine Small	intestine
18	chr11:65821400-65831800	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr11:65821400-65833800	Strong transcription	Placenta	Placenta
20	chr11:65821400-65835200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr11:65821400-65835200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr11:65821400-65835400	Strong transcription	Stomach Smooth Muscle	stomach
23	chr11:65821400-65835600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:65821400-65835600	Strong transcription	Brain Germinal Matrix	brain
25	chr11:65821400-65835800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr11:65821400-65836600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr11:65821600-65829200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:65821600-65835400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:65821600-65835400	Strong transcription	Fetal Thymus	thymus
30	chr11:65821600-65836000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:65821800-65831800	Strong transcription	Lung	lung
32	chr11:65821800-65832000	Strong transcription	Brain Cingulate Gyrus	brain
33	chr11:65821800-65832800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr11:65821800-65833600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:65821800-65833800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr11:65821800-65835400	Strong transcription	Spleen	Spleen
37	chr11:65821800-65835800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr11:65821800-65835800	Strong transcription	K562	blood
39	chr11:65821800-65836000	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr11:65821800-65836000	Strong transcription	Primary T cells from cord blood	blood
41	chr11:65821800-65836600	Strong transcription	Thymus	Thymus
42	chr11:65822000-65831600	Strong transcription	Esophagus	oesophagus
43	chr11:65822000-65831600	Strong transcription	Right Ventricle	heart
44	chr11:65822000-65831600	Strong transcription	HSMMtube	muscle
45	chr11:65822000-65832200	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr11:65822000-65832400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr11:65822000-65833000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:65822000-65833000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
49	chr11:65822000-65833000	Strong transcription	Left Ventricle	heart
50	chr11:65822000-65833200	Strong transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links