Variant report

Variant	rs1153976
Chromosome Location	chr12:48002400-48002401
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:47995378..47998174-chr12:48001804..48005197,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10082722	0.84[ASN][1000 genomes]
rs10083203	0.84[ASN][1000 genomes]
rs10875668	0.82[ASN][1000 genomes]
rs10875672	0.84[ASN][1000 genomes]
rs11168172	0.82[ASN][1000 genomes]
rs11168174	0.84[ASN][1000 genomes]
rs11534912	0.87[ASN][1000 genomes]
rs1232979	0.83[ASN][1000 genomes]
rs1233051	0.89[EUR][1000 genomes]
rs1233062	0.82[CEU][hapmap]
rs1237844	1.00[CEU][hapmap];0.93[CHB][hapmap];0.83[EUR][1000 genomes]
rs2057730	1.00[CHB][hapmap];0.93[CHD][hapmap]
rs2239187	0.86[CHB][hapmap]
rs2285831	0.86[CHB][hapmap]
rs2524319	0.86[EUR][1000 genomes]
rs2525450	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3809318	0.93[CHB][hapmap]
rs61917589	0.88[EUR][1000 genomes]
rs7298493	0.82[ASN][1000 genomes]
rs73113128	0.84[ASN][1000 genomes]
rs7312135	1.00[CHB][hapmap];0.93[CHD][hapmap]
rs7314657	0.84[ASN][1000 genomes]
rs7960755	1.00[CHB][hapmap]
rs929269	0.86[CHB][hapmap]
rs9668083	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558785	chr12:47740440-48044011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv832400	chr12:47840248-48024605	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv430507	chr12:47883933-48079507	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1051131	chr12:47883981-48016556	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv899056	chr12:47940764-48012390	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv558786	chr12:47942029-48044011	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv558788	chr12:47945797-48012390	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv2761737	chr12:47946795-48045722	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1053061	chr12:47946795-48045722	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv899057	chr12:47947551-48012390	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1050043	chr12:47949004-48087218	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv527728	chr12:47954597-48044506	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1153976	WNT1	cis	parietal	SCAN
rs1153976	SENP1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47992600-48006600	Weak transcription	HSMMtube	muscle
2	chr12:47996000-48006800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:47997000-48005000	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:47998800-48030800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:47999200-48002600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:47999600-48006400	Weak transcription	Primary T cells from cord blood	blood
7	chr12:48000800-48002600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:48001000-48002600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr12:48001000-48004400	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr12:48001400-48002600	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr12:48001600-48002400	Enhancers	Primary hematopoietic stem cells	blood
12	chr12:48001600-48002600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr12:48001600-48002600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr12:48001800-48002600	Enhancers	Primary B cells from cord blood	blood
15	chr12:48001800-48002600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:48001800-48002800	Weak transcription	Psoas Muscle	Psoas
17	chr12:48001800-48006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:48002000-48003600	Weak transcription	Fetal Muscle Leg	muscle
19	chr12:48002000-48004000	Enhancers	Primary B cells from peripheral blood	blood
20	chr12:48002000-48005800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:48002000-48006800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:48002400-48003600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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