Variant report

Variant	rs11112163
Chromosome Location	chr12:105072509-105072510
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105064637..105067234-chr12:105069243..105072797,3	MCF-7	breast:
2	chr12:105071012..105073165-chr12:105077860..105080234,2	MCF-7	breast:
3	chr12:105061726..105063507-chr12:105070074..105072816,2	MCF-7	breast:
4	chr12:105071577..105074645-chr12:105076983..105080645,3	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 31 )

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

rs_ID	r²[population]
rs10861268	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10861269	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs11112155	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs11112156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11112157	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11112158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11112159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112161	1.00[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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112164	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs11112165	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs11112166	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11112167	1.00[TSI][hapmap]
rs11112168	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11112169	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12581027	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs703668	0.88[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs703669	0.88[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs703670	0.88[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs703673	0.88[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs703674	0.88[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs703675	0.88[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs703679	0.88[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap]
rs7133386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1050695	chr12:105000981-105125161	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv541589	chr12:105000981-105125161	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs11112163	OMD	trans	brain	seeQTL
rs11112163	SFRP2	trans	brain	seeQTL
rs11112163	C2orf40	trans	brain	seeQTL
rs11112163	FZD1	trans	brain	seeQTL
rs11112163	FGL2	trans	brain	seeQTL
rs11112163	PHLDB2	trans	brain	seeQTL
rs11112163	ENPP6	trans	brain	seeQTL
rs11112163	SLC26A2	trans	brain	seeQTL
rs11112163	TMEM30B	trans	brain	seeQTL
rs11112163	TNFRSF11B	trans	brain	seeQTL
rs11112163	PDGFD	trans	brain	seeQTL
rs11112163	KLF5	trans	brain	seeQTL
rs11112163	FMOD	trans	brain	seeQTL
rs11112163	BMP5	trans	brain	seeQTL
rs11112163	KLF4	trans	brain	seeQTL
rs11112163	PTGDS	trans	brain	seeQTL
rs11112163	UPK1B	trans	brain	seeQTL
rs11112163	C19orf33	trans	brain	seeQTL
rs11112163	SLPI	trans	brain	seeQTL
rs11112163	GYPC	trans	brain	seeQTL
rs11112163	PRRX2	trans	brain	seeQTL
rs11112163	OLFML2A	trans	brain	seeQTL
rs11112163	SLC47A1	trans	brain	seeQTL
rs11112163	PDGFRL	trans	brain	seeQTL
rs11112163	FOXD1	trans	brain	seeQTL
rs11112163	PERP	trans	brain	seeQTL
rs11112163	PTGDR	trans	brain	seeQTL
rs11112163	LRRN4CL	trans	brain	seeQTL
rs11112163	COL6A2	trans	brain	seeQTL
rs11112163	LTBP2	trans	brain	seeQTL
rs11112163	KLK1	trans	brain	seeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105065400-105076000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:105065600-105075400	Weak transcription	Primary T cells from cord blood	blood
3	chr12:105066000-105072800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:105066000-105073000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:105066000-105073600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:105066000-105073800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:105066000-105074000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:105066000-105074000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:105066200-105073200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr12:105066200-105073600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr12:105066200-105074200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:105066200-105074200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:105066400-105074200	Weak transcription	Thymus	Thymus
14	chr12:105066600-105073400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:105066600-105073400	Weak transcription	Spleen	Spleen
16	chr12:105066600-105077800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:105066800-105073400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr12:105067600-105076400	Weak transcription	Brain Anterior Caudate	brain
19	chr12:105067800-105073600	Weak transcription	Fetal Thymus	thymus
20	chr12:105067800-105076200	Weak transcription	Right Ventricle	heart
21	chr12:105067800-105076600	Weak transcription	Left Ventricle	heart
22	chr12:105067800-105078600	Weak transcription	Brain Substantia Nigra	brain
23	chr12:105067800-105096000	Weak transcription	K562	blood
24	chr12:105068000-105072800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:105068000-105073000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:105068000-105073800	Weak transcription	HSMMtube	muscle
27	chr12:105068000-105076000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:105068000-105077600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:105068200-105074000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:105068200-105078600	Weak transcription	NHDF-Ad	bronchial
31	chr12:105068400-105073400	Weak transcription	A549	lung
32	chr12:105068400-105076200	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:105069200-105073800	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr12:105069400-105074200	Genic enhancers	Dnd41	blood
35	chr12:105069400-105076400	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr12:105069800-105074600	Enhancers	Placenta	Placenta
37	chr12:105070000-105073000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:105070600-105074800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr12:105070600-105076400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr12:105070800-105073000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr12:105070800-105073200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr12:105070800-105076600	Weak transcription	Lung	lung
43	chr12:105071200-105076000	Weak transcription	Fetal Stomach	stomach
44	chr12:105071200-105085800	Weak transcription	Brain Hippocampus Middle	brain
45	chr12:105071400-105073000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:105071400-105073400	Weak transcription	Primary B cells from cord blood	blood
47	chr12:105071600-105073200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:105071600-105073200	Weak transcription	Fetal Muscle Leg	muscle
49	chr12:105071800-105072800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:105071800-105073000	Weak transcription	Fetal Muscle Trunk	muscle

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