Variant report

Variant	rs12569193
Chromosome Location	chr1:151115186-151115187
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:10)
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	SPI1	chr1:151114872-151115189	GM12891	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151112727..151117017-chr1:151118116..151120270,3	K562	blood:
2	chr1:151032560..151034898-chr1:151112557..151115397,2	MCF-7	breast:
3	chr1:151110135..151112456-chr1:151113233..151115304,2	K562	blood:
4	chr1:151029687..151031858-chr1:151114009..151116505,2	K562	blood:
5	chr1:151114895..151122057-chr1:151125026..151130825,9	MCF-7	breast:
6	chr1:151115125..151117967-chr1:151253558..151255357,2	K562	blood:
7	chr1:151114839..151116907-chr1:151121689..151124445,2	K562	blood:
8	chr1:151109028..151112291-chr1:151113939..151118222,5	K562	blood:
9	chr1:151114749..151117567-chr1:151151983..151153922,2	K562	blood:
10	chr1:151040013..151045011-chr1:151111761..151118476,6	MCF-7	breast:

No data

Variant related genes	Relation type
SEMA6C	TF binding region
ENSG00000143373	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000143434	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000163154	Chromatin interaction
ENSG00000232671	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 19 )

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

rs_ID	r²[population]
rs10788798	0.86[JPT][hapmap]
rs10788800	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10888405	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11204777	0.86[JPT][hapmap]
rs11204780	0.86[JPT][hapmap]
rs11204782	0.85[JPT][hapmap]
rs11807526	0.86[JPT][hapmap]
rs12087892	0.86[JPT][hapmap]
rs1524773	0.85[JPT][hapmap]
rs15740	0.84[GIH][hapmap]
rs2067606	0.86[JPT][hapmap]
rs2091219	0.88[CEU][hapmap];0.88[MEX][hapmap]
rs2140709	0.86[JPT][hapmap]
rs3738481	0.85[JPT][hapmap]
rs4357530	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4360524	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4512652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970941	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs4970993	0.86[JPT][hapmap]
rs4970998	0.86[JPT][hapmap]
rs4971005	0.86[JPT][hapmap]
rs4971007	0.86[JPT][hapmap]
rs4971008	0.86[JPT][hapmap]
rs61819219	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6656450	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6674970	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6676190	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes]
rs7522608	0.81[EUR][1000 genomes]
rs7523731	0.86[JPT][hapmap]
rs7546304	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7554936	0.96[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]

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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv872422	chr1:151098077-151115186	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv872423	chr1:151100612-151115997	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs12569193	GABPB2	cis	cerebellum	SCAN
rs12569193	LYSMD1	cis	brain	BrainEAC
rs12569193	LYSMD1	cis	temporal cortex	BrainEAC
rs12569193	LYSMD1	cis	cerebellar cortex	BrainEAC
rs12569193	PEX11B	cis	parietal	SCAN
rs12569193	PRPF3	cis	parietal	SCAN
rs12569193	LYSMD1	cis	intralobular white matter	BrainEAC
rs12569193	CDC42SE1	cis	lymphoblastoid	seeQTL
rs12569193	CDC42SE1	cis	parietal	SCAN
rs12569193	LYSMD1	cis	occipital cortex	BrainEAC
rs12569193	LYSMD1	cis	hippocampus	BrainEAC
rs12569193	PRPF3	cis	cerebellum	SCAN
rs12569193	LYSMD1	cis	parietal	SCAN
rs12569193	LYSMD1	cis	substantia nigra	BrainEAC
rs12569193	LYSMD1	cis	frontal cortex	BrainEAC
rs12569193	BNIPL	cis	lung	GTEx
rs12569193	ZNF687	cis	cerebellum	SCAN
rs12569193	LYSMD1	cis	thalamus	BrainEAC
rs12569193	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151104400-151116600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr1:151104400-151117000	Weak transcription	Fetal Kidney	kidney
3	chr1:151104400-151118000	Weak transcription	Aorta	Aorta
4	chr1:151104600-151117400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:151104600-151118200	Weak transcription	Primary T cells from cord blood	blood
6	chr1:151104800-151115600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:151105000-151115400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:151105000-151115600	Weak transcription	Fetal Thymus	thymus
9	chr1:151105200-151115200	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:151105200-151115400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:151105200-151117000	Weak transcription	Placenta	Placenta
12	chr1:151105400-151117000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:151105600-151115800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:151105600-151118000	Weak transcription	Gastric	stomach
15	chr1:151105800-151115600	Weak transcription	Thymus	Thymus
16	chr1:151105800-151117200	Weak transcription	Spleen	Spleen
17	chr1:151106200-151116000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:151106600-151115400	Strong transcription	Fetal Stomach	stomach
19	chr1:151106600-151116000	Strong transcription	Fetal Intestine Small	intestine
20	chr1:151107000-151116600	Weak transcription	HUVEC	blood vessel
21	chr1:151107000-151117600	Weak transcription	Colonic Mucosa	Colon
22	chr1:151107800-151115800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:151108400-151115400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:151108400-151117200	Weak transcription	Brain Substantia Nigra	brain
25	chr1:151108600-151117800	Weak transcription	Esophagus	oesophagus
26	chr1:151108800-151115600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:151109400-151115200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:151109400-151115400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:151109400-151116000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:151109600-151115400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:151109600-151115600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:151109600-151116200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:151109600-151117600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:151110200-151115600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:151110200-151117600	Weak transcription	Pancreas	Pancrea
36	chr1:151110800-151116200	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:151112200-151115600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:151112400-151115800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:151112400-151116200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:151112600-151115600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:151112600-151115600	Weak transcription	Lung	lung
42	chr1:151112800-151116600	Weak transcription	Brain Anterior Caudate	brain
43	chr1:151112800-151116600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:151112800-151117400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr1:151113000-151115600	Weak transcription	Adipose Nuclei	Adipose
46	chr1:151113000-151115600	Weak transcription	Fetal Lung	lung
47	chr1:151113000-151115800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr1:151113000-151115800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:151113000-151116000	Weak transcription	Brain Angular Gyrus	brain
50	chr1:151113000-151116400	Weak transcription	Ovary	ovary

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