Variant report

Variant	rs10512249
Chromosome Location	chr9:98256309-98256310
allele	C/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	chr9:98256239-98256594	SK-N-SH	brain:	n/a	n/a
2	MAX	chr9:98256171-98257691	NB4	blood:	n/a	chr9:98256459-98256469 chr9:98256240-98256249
3	POLR2A	chr9:98256062-98257543	GM12892	blood:	n/a	n/a
4	MYC	chr9:98256207-98257677	NB4	blood:	n/a	chr9:98256459-98256469 chr9:98256240-98256249
5	POLR2A	chr9:98256061-98257051	SK-N-SH	brain:	n/a	n/a
6	REST	chr9:98256163-98257039	SK-N-SH	brain:	n/a	chr9:98256817-98256837 chr9:98256817-98256826 chr9:98256185-98256205 chr9:98256817-98256837 chr9:98256185-98256205
7	POLR2A	chr9:98256177-98257662	GM12892	blood:	n/a	n/a
8	MAX	chr9:98256034-98257145	SK-N-SH	brain:	n/a	chr9:98256459-98256469 chr9:98256240-98256249
9	PBX3	chr9:98256114-98257011	SK-N-SH	brain:	n/a	n/a
10	PBX3	chr9:98256220-98256851	SK-N-SH	brain:	n/a	n/a
11	USF1	chr9:98256186-98256811	SK-N-SH	brain:	n/a	chr9:98256470-98256486 chr9:98256459-98256475
12	PAX5	chr9:98256268-98257049	GM12892	blood:	n/a	chr9:98256942-98256951 chr9:98256854-98256873 chr9:98256412-98256421 chr9:98256909-98256918
13	POLR2A	chr9:98256190-98256743	Gliobla	brain:	n/a	n/a
14	EBF1	chr9:98256309-98257027	GM12878	blood:	n/a	n/a
15	TAF1	chr9:98256229-98256544	SK-N-SH	brain:	n/a	n/a
16	USF1	chr9:98256222-98256539	SK-N-SH_RA	brain:	n/a	chr9:98256470-98256486 chr9:98256459-98256475
17	POLR2A	chr9:98256138-98256569	U87	brain:	n/a	n/a
18	USF1	chr9:98256220-98256543	SK-N-SH_RA	brain:	n/a	chr9:98256470-98256486 chr9:98256459-98256475
19	MAX	chr9:98256218-98257508	GM12878	blood:	n/a	chr9:98256459-98256469 chr9:98256240-98256249
20	NRF1	chr9:98255996-98257314	SK-N-SH	brain:	n/a	chr9:98256402-98256416 chr9:98256436-98256445 chr9:98256434-98256448 chr9:98256434-98256445 chr9:98256434-98256443 chr9:98256405-98256416 chr9:98256458-98256467 chr9:98256431-98256445 chr9:98256405-98256419 chr9:98256405-98256414
21	MAX	chr9:98256041-98257137	SK-N-SH	brain:	n/a	chr9:98256459-98256469 chr9:98256240-98256249
22	POLR2A	chr9:98256269-98257027	GM12878	blood:	n/a	n/a
23	TCF3	chr9:98256234-98257005	GM12878	blood:	n/a	chr9:98256373-98256386
24	ELF1	chr9:98256220-98257173	GM12878	blood:	n/a	chr9:98256905-98256918
25	REST	chr9:98256055-98257067	SK-N-SH	brain:	n/a	chr9:98256817-98256837 chr9:98256817-98256826 chr9:98256185-98256205 chr9:98256817-98256837 chr9:98256185-98256205
26	MXI1	chr9:98255701-98258478	SK-N-SH	brain:	n/a	chr9:98256240-98256255 chr9:98256344-98256353
27	CTCF	chr9:98256300-98256450	SK-N-SH_RA	brain:	n/a	n/a
28	GATA2	chr9:98256272-98256788	SH-SY5Y	brain:	n/a	chr9:98256490-98256499 chr9:98256491-98256508
29	CTCF	chr9:98256240-98256390	WERI-Rb-1	eye:	n/a	n/a
30	POLR2A	chr9:98256214-98257161	GM12892	blood:	n/a	n/a
31	BHLHE40	chr9:98256264-98257261	GM12878	blood:	n/a	chr9:98256470-98256486 chr9:98256459-98256475
32	WRNIP1	chr9:98256157-98256327	GM12878	blood:	n/a	n/a
33	NRF1	chr9:98256256-98257364	GM12878	blood:	n/a	chr9:98256402-98256416 chr9:98256436-98256445 chr9:98256434-98256448 chr9:98256434-98256445 chr9:98256434-98256443 chr9:98256405-98256416 chr9:98256458-98256467 chr9:98256431-98256445 chr9:98256405-98256419 chr9:98256405-98256414
34	POLR2A	chr9:98256132-98256766	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98254778..98257186-chr9:98269292..98272061,2	MCF-7	breast:
2	chr9:98253772..98257280-chr9:98266534..98270044,4	K562	blood:

Variant related genes	Relation type
ENSG00000271314	TF binding region
ENSG00000271155	Chromatin interaction
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs16909856	0.82[CEU][hapmap]
rs16909859	0.82[CEU][hapmap]
rs16909865	0.85[CHB][hapmap]
rs16909892	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs16909898	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909904	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909922	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16909927	0.84[CEU][hapmap]
rs1805155	0.87[ASW][hapmap];0.91[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2036963	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282040	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282041	1.00[ASW][hapmap];0.91[CEU][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2282043	0.91[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28372566	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28377268	0.85[EUR][1000 genomes]
rs28418339	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427480	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28446116	0.87[ASW][hapmap];0.91[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28446321	0.96[EUR][1000 genomes]
rs28448271	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28457693	0.86[EUR][1000 genomes]
rs28469297	0.84[CEU][hapmap];1.00[MEX][hapmap]
rs28474857	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493225	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28494679	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs28510415	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28520225	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28520360	0.84[CEU][hapmap]
rs28535536	0.87[ASW][hapmap];0.91[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs28583690	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28673156	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28706464	0.87[ASW][hapmap];0.91[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28711421	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780573	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3824488	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56149656	0.87[EUR][1000 genomes]
rs59015093	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59925771	0.95[EUR][1000 genomes]
rs60150206	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60417486	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs867452	0.82[AFR][1000 genomes];0.87[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	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv1051665	chr9:98234404-98264577	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv824994	chr9:98239963-98314431	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv824995	chr9:98243455-98326547	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv824996	chr9:98245375-98283861	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1053434	chr9:98248328-98259178	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10512249	FBP2	cis	parietal	SCAN
rs10512249	PTCH1	cis	lymphoblastoid	seeQTL
rs10512249	PTCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
2	chr9:98232200-98261200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr9:98239800-98260000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:98240200-98267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:98240800-98259800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:98241000-98258400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:98242000-98256400	Weak transcription	Esophagus	oesophagus
8	chr9:98242400-98266400	Weak transcription	HSMMtube	muscle
9	chr9:98242800-98256600	Weak transcription	Fetal Kidney	kidney
10	chr9:98242800-98266600	Weak transcription	Adipose Nuclei	Adipose
11	chr9:98243000-98256800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:98243000-98267800	Weak transcription	Aorta	Aorta
13	chr9:98243400-98256400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:98243600-98256400	Weak transcription	HepG2	liver
15	chr9:98243800-98260000	Weak transcription	HSMM	muscle
16	chr9:98244400-98256600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr9:98244800-98257000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr9:98245000-98256800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr9:98245200-98256600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr9:98246600-98259600	Weak transcription	Right Atrium	heart
21	chr9:98246800-98256400	Weak transcription	Fetal Muscle Leg	muscle
22	chr9:98247000-98256600	Weak transcription	Fetal Heart	heart
23	chr9:98248000-98258400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:98249200-98256400	Weak transcription	Right Ventricle	heart
25	chr9:98249200-98263600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr9:98249400-98256400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr9:98249400-98257800	Weak transcription	Liver	Liver
28	chr9:98250400-98262800	Weak transcription	Stomach Mucosa	stomach
29	chr9:98251400-98256400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:98251600-98256600	Weak transcription	K562	blood
31	chr9:98251800-98256600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr9:98252600-98257200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr9:98252800-98256600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr9:98253400-98256800	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr9:98253400-98257000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr9:98253400-98261000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr9:98253400-98262400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr9:98253600-98256400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:98253600-98257400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:98253600-98257600	Strong transcription	Fetal Intestine Small	intestine
41	chr9:98253800-98256400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr9:98253800-98256600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr9:98253800-98256600	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr9:98253800-98257000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr9:98254000-98256400	Weak transcription	Gastric	stomach
46	chr9:98254000-98256400	Weak transcription	Left Ventricle	heart
47	chr9:98254000-98257000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr9:98254000-98267400	Weak transcription	Small Intestine	intestine
49	chr9:98254200-98256600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr9:98254200-98256800	Weak transcription	Ovary	ovary

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