Variant report

Variant	rs12068986
Chromosome Location	chr1:158091417-158091418
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:157939248..157940197-chr1:158091169..158092032,4	MCF-7	breast:
2	chr1:157933197..157933769-chr1:158090882..158091680,2	K562	blood:
3	chr1:157961469..157962519-chr1:158091157..158092029,5	MCF-7	breast:
4	chr1:158086077..158087753-chr1:158090145..158092458,2	K562	blood:
5	chr1:158073091..158075262-chr1:158089986..158091612,2	K562	blood:
6	chr1:158090190..158092923-chr1:179567746..179569277,2	MCF-7	breast:
7	chr1:157961452..157962372-chr1:158091311..158092049,2	K562	blood:
8	chr1:157961597..157962396-chr1:158090797..158092182,4	MCF-7	breast:
9	chr1:158056895..158057743-chr1:158091127..158091633,2	MCF-7	breast:
10	chr1:157939318..157940200-chr1:158091117..158092079,2	MCF-7	breast:

No data

Extended variants
information (count: 13 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12042149	0.84[ASN][1000 genomes]
rs12097784	0.84[ASN][1000 genomes]
rs16839865	0.84[ASN][1000 genomes]
rs1853687	0.84[ASN][1000 genomes]
rs1998639	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2093918	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656612	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656904	0.94[JPT][hapmap]
rs4656905	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs61321196	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66845334	0.84[ASN][1000 genomes]
rs6690094	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12068986	LCE3C	cis	cerebellum	SCAN
rs12068986	KRTCAP2	cis	cerebellum	SCAN
rs12068986	C1orf189	cis	parietal	SCAN
rs12068986	OR10J1	cis	cerebellum	SCAN
rs12068986	CRP	cis	parietal	SCAN
rs12068986	DENND4B	cis	parietal	SCAN
rs12068986	LCE1D	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158084000-158092600	Weak transcription	HMEC	breast
2	chr1:158084200-158091600	Weak transcription	Spleen	Spleen
3	chr1:158087200-158091800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:158088600-158091800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr1:158088800-158094000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:158090000-158091800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:158090200-158091600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:158090200-158091600	Weak transcription	Thymus	Thymus
9	chr1:158090400-158093600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:158090400-158093800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:158090400-158093800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:158090400-158094000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:158090400-158094000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:158090400-158094000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:158090800-158094000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:158091200-158092000	Enhancers	HSMMtube	muscle
17	chr1:158091400-158091600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr1:158091400-158091600	Enhancers	Fetal Intestine Large	intestine
19	chr1:158091400-158091600	Bivalent Enhancer	NHLF	lung
20	chr1:158091400-158091800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
21	chr1:158091400-158091800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:158091400-158091800	Bivalent Enhancer	Fetal Muscle Leg	muscle
23	chr1:158091400-158091800	Enhancers	Fetal Thymus	thymus
24	chr1:158091400-158091800	Enhancers	Pancreas	Pancrea
25	chr1:158091400-158091800	Bivalent Enhancer	A549	lung
26	chr1:158091400-158091800	Bivalent Enhancer	NHDF-Ad	bronchial
27	chr1:158091400-158091800	Enhancers	NHEK	skin
28	chr1:158091400-158092000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr1:158091400-158092000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr1:158091400-158092000	Bivalent Enhancer	HSMM	muscle

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