Variant report

Variant	rs1143901
Chromosome Location	chr12:32293659-32293660
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1143900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1673857	0.86[MEX][hapmap]
rs1684149	0.86[MEX][hapmap]
rs1809241	0.95[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs2608404	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2652019	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2668296	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2668297	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2668298	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7301601	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3363806	chr12:31872264-32410283	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3508621	chr12:31872654-32410593	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3508622	chr12:31872654-32410593	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv976030	chr12:32153446-32307541	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv983498	chr12:32153446-32388092	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv898969	chr12:32224948-32375677	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1042317	chr12:32228872-32316774	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1041733	chr12:32247427-32312547	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv558171	chr12:32287259-32559693	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1143901	FGD4	cis	cerebellum	SCAN
rs1143901	C12orf35	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32269000-32340200	Weak transcription	Dnd41	blood
2	chr12:32287600-32312200	Weak transcription	HSMMtube	muscle
3	chr12:32287800-32304000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:32287800-32328400	Weak transcription	Aorta	Aorta
5	chr12:32292000-32293800	Active TSS	Primary T cells from cord blood	blood
6	chr12:32292000-32294000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:32292000-32294200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:32292000-32294200	Active TSS	Ovary	ovary
9	chr12:32292200-32293800	Active TSS	Primary T cells fromperipheralblood	blood
10	chr12:32292200-32293800	Active TSS	Brain Angular Gyrus	brain
11	chr12:32292200-32293800	Active TSS	Brain Substantia Nigra	brain
12	chr12:32292200-32294000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:32292200-32294000	Active TSS	Right Atrium	heart
14	chr12:32292200-32294200	Active TSS	Brain Anterior Caudate	brain
15	chr12:32292200-32294200	Active TSS	Brain Cingulate Gyrus	brain
16	chr12:32292200-32294200	Flanking Active TSS	Fetal Brain Male	brain
17	chr12:32292200-32312200	Weak transcription	HSMM	muscle
18	chr12:32292400-32294000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:32292400-32294000	Active TSS	Fetal Brain Female	brain
20	chr12:32292400-32294000	Active TSS	Fetal Kidney	kidney
21	chr12:32292400-32294200	Active TSS	Brain Hippocampus Middle	brain
22	chr12:32292600-32293800	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr12:32292600-32294000	Active TSS	Adipose Nuclei	Adipose
24	chr12:32292600-32299200	Weak transcription	Fetal Heart	heart
25	chr12:32293000-32293800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr12:32293000-32293800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr12:32293000-32293800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr12:32293000-32293800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr12:32293000-32294000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr12:32293000-32294000	Enhancers	NH-A	brain
31	chr12:32293000-32294200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr12:32293000-32295600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:32293000-32295600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:32293000-32301000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:32293000-32301200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:32293000-32306800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:32293000-32316000	Weak transcription	HUVEC	blood vessel
38	chr12:32293200-32293800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:32293200-32293800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:32293200-32293800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:32293200-32293800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr12:32293200-32294000	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr12:32293200-32294000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr12:32293200-32294000	Enhancers	Primary B cells from peripheral blood	blood
45	chr12:32293200-32294200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:32293200-32298800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:32293200-32301000	Weak transcription	Osteobl	bone
48	chr12:32293200-32301400	Weak transcription	NHEK	skin
49	chr12:32293200-32301800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:32293200-32302600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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