Variant report

Variant	rs12810608
Chromosome Location	chr12:85674707-85674708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10160886	0.82[GIH][hapmap]
rs11116771	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12315575	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1507209	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs1512732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1512733	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs2660449	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs359992	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs4074726	0.92[GIH][hapmap];0.87[TSI][hapmap]
rs4076027	0.96[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6539889	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7486483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7488598	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs777035	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs796567	0.81[CHB][hapmap];0.84[JPT][hapmap]

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	nsv1040452	chr12:85179586-85747907	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv1792335	chr12:85321249-86003609	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv899388	chr12:85427691-85766847	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1040622	chr12:85502226-85693132	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv541558	chr12:85502226-85693132	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv559662	chr12:85544429-85734069	Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv817242	chr12:85622245-86069213	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv2761757	chr12:85626466-85741934	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv899392	chr12:85638089-85734069	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv533923	chr12:85647133-85713608	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1054573	chr12:85658602-86235433	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1035600	chr12:85661373-86235433	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv899393	chr12:85674707-85796968	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12810608	ALX1	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:85672000-85675400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr12:85672600-85676200	Active TSS	Hela-S3	cervix
3	chr12:85672800-85675400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr12:85673000-85675000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:85673000-85675200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:85673000-85676200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:85673000-85679400	Bivalent/Poised TSS	Fetal Kidney	kidney
8	chr12:85673200-85674800	Bivalent/Poised TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:85673200-85674800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
10	chr12:85673200-85675000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:85673200-85675200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:85673200-85675800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:85673400-85674800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:85673400-85674800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
15	chr12:85673400-85674800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:85673400-85674800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
17	chr12:85673400-85675200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:85673400-85675200	Active TSS	H9 Cell Line	embryonic stem cell
19	chr12:85673400-85675800	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr12:85673600-85674800	Active TSS	HUVEC	blood vessel
21	chr12:85673600-85674800	Flanking Bivalent TSS/Enh	NH-A	brain
22	chr12:85673600-85675000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:85673600-85675200	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr12:85673600-85675400	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr12:85673600-85675400	Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr12:85673600-85675600	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr12:85673800-85674800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:85673800-85674800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:85673800-85674800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:85673800-85674800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
31	chr12:85673800-85674800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
32	chr12:85673800-85674800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
33	chr12:85673800-85675000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
34	chr12:85673800-85675200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
35	chr12:85673800-85675400	Active TSS	H1 Cell Line	embryonic stem cell
36	chr12:85673800-85675400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:85673800-85675400	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr12:85673800-85675800	Bivalent/Poised TSS	NHDF-Ad	bronchial
39	chr12:85673800-85676000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:85674000-85674800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
41	chr12:85674000-85674800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:85674000-85674800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
43	chr12:85674000-85674800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
44	chr12:85674000-85674800	Flanking Bivalent TSS/Enh	Placenta	Placenta
45	chr12:85674000-85674800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
46	chr12:85674000-85674800	Flanking Bivalent TSS/Enh	NHEK	skin
47	chr12:85674000-85674800	Bivalent/Poised TSS	NHLF	lung
48	chr12:85674000-85675000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:85674000-85675000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
50	chr12:85674000-85675000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle

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