Variant report

Variant	rs12087892
Chromosome Location	chr1:151118500-151118501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151103786..151106331-chr1:151117499..151120768,3	MCF-7	breast:
2	chr1:151096194..151098701-chr1:151116242..151118774,2	MCF-7	breast:
3	chr1:151102270..151104122-chr1:151117546..151119575,3	K562	blood:
4	chr1:151114895..151122057-chr1:151125026..151130825,9	MCF-7	breast:
5	chr1:151008899..151010447-chr1:151116259..151119248,2	MCF-7	breast:
6	chr1:151117604..151120749-chr1:151128246..151131666,4	MCF-7	breast:
7	chr1:151117625..151120818-chr1:151135402..151140051,4	MCF-7	breast:
8	chr1:151106109..151110392-chr1:151117941..151122227,5	K562	blood:
9	chr1:151104617..151106812-chr1:151117447..151119044,2	MCF-7	breast:
10	chr1:151118376..151121066-chr1:151225165..151227350,2	MCF-7	breast:
11	chr1:151117616..151120860-chr1:151252294..151255501,4	K562	blood:
12	chr1:151106109..151108676-chr1:151117941..151119953,3	K562	blood:
13	chr1:151112451..151114462-chr1:151116329..151118583,3	K562	blood:
14	chr1:151116657..151121305-chr1:151127749..151129795,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000232671	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000143434	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000163141	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000261168	Chromatin interaction
ENSG00000163154	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10788798	1.00[JPT][hapmap]
rs11204777	1.00[JPT][hapmap]
rs11204780	1.00[JPT][hapmap]
rs11204782	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577302	0.85[CHB][hapmap]
rs11807526	1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11807847	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12569193	0.86[JPT][hapmap]
rs1524773	1.00[JPT][hapmap]
rs16833107	0.85[CHB][hapmap]
rs1752388	0.85[CHB][hapmap]
rs1780586	0.85[CHB][hapmap]
rs2067606	0.94[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2140709	1.00[JPT][hapmap]
rs2298265	0.85[CHB][hapmap]
rs35118469	0.85[CHB][hapmap]
rs3738481	1.00[JPT][hapmap]
rs3748545	0.85[CHB][hapmap]
rs3811402	1.00[ASN][1000 genomes]
rs41305062	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4357530	0.86[JPT][hapmap]
rs4512652	0.86[JPT][hapmap]
rs4970941	0.86[JPT][hapmap]
rs4970993	1.00[JPT][hapmap]
rs4970998	1.00[JPT][hapmap]
rs4971005	1.00[JPT][hapmap]
rs4971007	1.00[JPT][hapmap]
rs4971008	1.00[JPT][hapmap]
rs56033976	0.89[ASN][1000 genomes]
rs56090305	0.88[ASN][1000 genomes]
rs56299877	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59578580	0.82[ASN][1000 genomes]
rs6587557	0.86[JPT][hapmap]
rs6656450	0.86[JPT][hapmap]
rs6674970	0.86[JPT][hapmap]
rs6676190	1.00[JPT][hapmap]
rs7522302	0.89[ASN][1000 genomes]
rs7523731	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7554936	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12087892	CDC42SE1	cis	parietal	SCAN
rs12087892	GOLPH3L	cis	cerebellum	SCAN
rs12087892	PEX11B	cis	parietal	SCAN
rs12087892	ZNF687	cis	cerebellum	SCAN
rs12087892	PIP5K1A	cis	cerebellum	SCAN
rs12087892	GABPB2	cis	cerebellum	SCAN
rs12087892	SEMA6C	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151115000-151118600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr1:151115600-151118800	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr1:151116400-151118800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:151116600-151118800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:151116800-151118600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
6	chr1:151117000-151118800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr1:151117000-151119600	Active TSS	Fetal Kidney	kidney
8	chr1:151117200-151118600	Flanking Active TSS	Fetal Muscle Leg	muscle
9	chr1:151117200-151118800	Flanking Active TSS	HUVEC	blood vessel
10	chr1:151117200-151119000	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr1:151117200-151119600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:151117200-151119600	Active TSS	Brain Angular Gyrus	brain
13	chr1:151117400-151118600	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr1:151117400-151118600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
15	chr1:151117400-151118800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:151117400-151119600	Active TSS	Fetal Brain Male	brain
17	chr1:151117400-151119600	Active TSS	Fetal Brain Female	brain
18	chr1:151117400-151119600	Active TSS	HSMMtube	muscle
19	chr1:151117400-151120200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:151117600-151118600	Flanking Active TSS	HSMM	muscle
21	chr1:151117600-151118800	Flanking Active TSS	Fetal Intestine Large	intestine
22	chr1:151117600-151119000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:151117600-151119000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
24	chr1:151117600-151119200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
25	chr1:151117600-151119600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:151117600-151119600	Active TSS	H9 Cell Line	embryonic stem cell
27	chr1:151117600-151119600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:151117600-151119600	Active TSS	Left Ventricle	heart
29	chr1:151117800-151118600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
30	chr1:151117800-151118800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:151117800-151119000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:151117800-151119600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr1:151117800-151119600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
34	chr1:151117800-151119600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr1:151117800-151119600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:151117800-151119600	Active TSS	Brain Substantia Nigra	brain
37	chr1:151117800-151119600	Active TSS	Esophagus	oesophagus
38	chr1:151117800-151119600	Active TSS	Fetal Heart	heart
39	chr1:151117800-151120000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr1:151118000-151118600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
41	chr1:151118000-151118600	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr1:151118000-151118800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:151118000-151118800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:151118000-151118800	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr1:151118000-151118800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr1:151118000-151118800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:151118000-151118800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:151118000-151118800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
49	chr1:151118000-151119000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
50	chr1:151118000-151119000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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