Variant report

Variant	rs547404
Chromosome Location	chr11:65824472-65824473
allele	A/G
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	chr11:65824119-65824526	K562	blood:	n/a	n/a
2	POLR2A	chr11:65824027-65824491	GM12892	blood:	n/a	n/a
3	POLR2A	chr11:65824017-65824491	K562	blood:	n/a	n/a
4	POLR2A	chr11:65823938-65824563	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:65656005..65658506-chr11:65823963..65825663,2	MCF-7	breast:
2	chr11:65822840..65824603-chr11:65843148..65845154,2	MCF-7	breast:
3	chr1:109203361..109204275-chr11:65824383..65825152,2	MCF-7	breast:

Variant related genes	Relation type
SF3B2	TF binding region
ENSG00000162639	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000175602	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1049872	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1203998	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12416952	0.82[ASN][1000 genomes]
rs12416953	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12421022	0.82[ASN][1000 genomes]
rs12803276	0.93[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1893316	0.93[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.86[ASN][1000 genomes]
rs2000672	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2452680	0.93[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33988687	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34073119	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34114713	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34123790	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35611816	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs477280	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs491618	0.95[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930333	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs503156	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs535752	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	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs570887	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs574153	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61895579	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7480811	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs947847	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv897770	chr11:65803750-65824472	Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv3349342	chr11:65824433-65824920	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs547404	SF3B2	cis	cerebellum	SCAN
rs547404	SF3B2	cis	parietal	SCAN
rs547404	SF3B2	cis	Whole Blood	GTEx
rs547404	SLC22A6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65820800-65827600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:65821000-65825000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:65821000-65835600	Weak transcription	Right Atrium	heart
4	chr11:65821000-65836600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:65821000-65836600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:65821200-65824600	Genic enhancers	Adipose Nuclei	Adipose
7	chr11:65821200-65828200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr11:65821200-65829000	Weak transcription	Fetal Heart	heart
9	chr11:65821200-65832000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:65821200-65832200	Strong transcription	Fetal Muscle Leg	muscle
11	chr11:65821200-65835400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr11:65821200-65835600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:65821200-65836000	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr11:65821200-65836000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr11:65821200-65836000	Strong transcription	Fetal Intestine Large	intestine
16	chr11:65821200-65836000	Strong transcription	NHLF	lung
17	chr11:65821200-65836200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr11:65821200-65836600	Strong transcription	Fetal Stomach	stomach
19	chr11:65821400-65825600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:65821400-65826200	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr11:65821400-65826400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:65821400-65827800	Weak transcription	Fetal Brain Male	brain
23	chr11:65821400-65830400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr11:65821400-65831400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:65821400-65831800	Strong transcription	Fetal Intestine Small	intestine
26	chr11:65821400-65831800	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr11:65821400-65833800	Strong transcription	Placenta	Placenta
28	chr11:65821400-65835200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr11:65821400-65835200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr11:65821400-65835400	Strong transcription	Stomach Smooth Muscle	stomach
31	chr11:65821400-65835600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr11:65821400-65835600	Strong transcription	Brain Germinal Matrix	brain
33	chr11:65821400-65835800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr11:65821400-65836600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:65821600-65829200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:65821600-65835400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr11:65821600-65835400	Strong transcription	Fetal Thymus	thymus
38	chr11:65821600-65836000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:65821800-65831800	Strong transcription	Lung	lung
40	chr11:65821800-65832000	Strong transcription	Brain Cingulate Gyrus	brain
41	chr11:65821800-65832800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
42	chr11:65821800-65833600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:65821800-65833800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr11:65821800-65835400	Strong transcription	Spleen	Spleen
45	chr11:65821800-65835800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr11:65821800-65835800	Strong transcription	K562	blood
47	chr11:65821800-65836000	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr11:65821800-65836000	Strong transcription	Primary T cells from cord blood	blood
49	chr11:65821800-65836600	Strong transcription	Thymus	Thymus
50	chr11:65822000-65827200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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