Variant report

Variant	rs574153
Chromosome Location	chr11:65817307-65817308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr11:65816095-65817543	SK-N-SH	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65816864..65823380-chr11:65832037..65840391,16	MCF-7	breast:
2	chr11:65815755..65817643-chr11:65824543..65827517,2	MCF-7	breast:
3	chr11:65812475..65816551-chr11:65816982..65820716,11	MCF-7	breast:
4	chr11:65792176..65796965-chr11:65812595..65817477,5	MCF-7	breast:
5	chr11:65815354..65817680-chr11:65821630..65823726,2	K562	blood:
6	chr11:65768250..65771590-chr11:65817294..65821421,6	K562	blood:
7	chr11:65811021..65815121-chr11:65816503..65821449,7	K562	blood:

No data

Variant related genes	Relation type
SF3B2	TF binding region
ENSG00000238752	TF binding region
GAL3ST3	TF binding region
ENSG00000255038	Chromatin interaction
ENSG00000175294	Chromatin interaction
ENSG00000087365	Chromatin interaction
ENSG00000175229	Chromatin interaction
ENSG00000175334	Chromatin interaction
ENSG00000175115	Chromatin interaction
ENSG00000175376	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1049872	0.84[EUR][1000 genomes]
rs1203998	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12803276	0.84[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs17147371	0.84[MEX][hapmap]
rs2000672	0.83[EUR][1000 genomes]
rs2452680	0.88[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs2576	0.80[MEX][hapmap]
rs33988687	0.84[EUR][1000 genomes]
rs34073119	0.83[EUR][1000 genomes]
rs34123790	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35611816	0.98[EUR][1000 genomes]
rs477280	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs491618	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs503156	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535752	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]
rs547404	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]
rs557799	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs570887	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7480811	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs873491	0.84[MEX][hapmap]
rs947847	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs574153	SLC22A6	cis	cerebellum	SCAN
rs574153	SF3B2	cis	cerebellum	SCAN
rs574153	SF3B2	cis	Whole Blood	GTEx
rs574153	SF3B2	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65790400-65818600	Weak transcription	HSMM	muscle
2	chr11:65813000-65818200	Weak transcription	Lung	lung
3	chr11:65813200-65818200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:65813200-65818200	Weak transcription	Spleen	Spleen
5	chr11:65813200-65818400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr11:65813200-65818800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr11:65813400-65817600	Weak transcription	K562	blood
8	chr11:65813400-65818200	Weak transcription	A549	lung
9	chr11:65813600-65818200	Weak transcription	Dnd41	blood
10	chr11:65814200-65819200	Enhancers	Pancreas	Pancrea
11	chr11:65814400-65818800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr11:65815800-65818200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr11:65815800-65818400	Weak transcription	Fetal Kidney	kidney
14	chr11:65816200-65817400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
15	chr11:65816400-65818400	Weak transcription	Right Ventricle	heart
16	chr11:65816600-65818200	Weak transcription	HMEC	breast
17	chr11:65816600-65818400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr11:65816600-65818400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:65816600-65818600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr11:65816600-65818600	Weak transcription	Brain Substantia Nigra	brain
21	chr11:65816600-65818600	Weak transcription	Left Ventricle	heart
22	chr11:65816600-65818800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr11:65816800-65818400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr11:65816800-65818400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:65816800-65818600	Weak transcription	Gastric	stomach
26	chr11:65817000-65817400	Enhancers	Thymus	Thymus
27	chr11:65817000-65817400	Bivalent Enhancer	HepG2	liver
28	chr11:65817000-65817600	Enhancers	H1 Cell Line	embryonic stem cell
29	chr11:65817000-65817600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:65817000-65818200	Weak transcription	Right Atrium	heart
31	chr11:65817000-65818600	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:65817000-65818800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr11:65817000-65819000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:65817000-65819000	Weak transcription	Primary T cells from cord blood	blood
35	chr11:65817000-65819000	Enhancers	Fetal Thymus	thymus
36	chr11:65817200-65817400	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr11:65817200-65817600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr11:65817200-65817600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:65817200-65817600	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr11:65817200-65817600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr11:65817200-65817600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:65817200-65818200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr11:65817200-65818200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr11:65817200-65818200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:65817200-65818200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr11:65817200-65818200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr11:65817200-65818200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr11:65817200-65818200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:65817200-65818200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:65817200-65818200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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