Variant report

Variant	rs10861347
Chromosome Location	chr12:105477410-105477411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10778367	1.00[CHB][hapmap]
rs10861371	1.00[CHB][hapmap]
rs11112434	1.00[CHB][hapmap]
rs1196748	1.00[CHB][hapmap]
rs1196749	1.00[CHB][hapmap]
rs1196753	1.00[CHB][hapmap]
rs1196754	1.00[CHB][hapmap]
rs1196755	0.85[CEU][hapmap]
rs1196756	1.00[CHB][hapmap]
rs1196760	1.00[CHB][hapmap]
rs1196777	1.00[CHB][hapmap]
rs1196793	1.00[CHB][hapmap]
rs1196800	1.00[CHB][hapmap]
rs1196801	1.00[CHB][hapmap]
rs1196806	1.00[CHB][hapmap]
rs1196813	1.00[CHB][hapmap]
rs1196817	1.00[CHB][hapmap]
rs1196818	1.00[CHB][hapmap]
rs1196819	1.00[CHB][hapmap]
rs1196839	1.00[CHB][hapmap]
rs1196842	1.00[CHB][hapmap]
rs1196848	1.00[CHB][hapmap]
rs1196852	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs1196861	1.00[CHB][hapmap]
rs1196862	1.00[CHB][hapmap]
rs1196864	1.00[CHB][hapmap]
rs1196881	1.00[CHB][hapmap]
rs1211276	1.00[CHB][hapmap]
rs12822081	1.00[CHB][hapmap]
rs1621553	1.00[CHB][hapmap]
rs1663564	1.00[CHB][hapmap]
rs2440715	1.00[CHB][hapmap]
rs4390426	1.00[CHB][hapmap]
rs7299166	0.94[CEU][hapmap]
rs935240	1.00[CHB][hapmap]
rs935241	1.00[CHB][hapmap]
rs935244	1.00[CHB][hapmap]

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	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10861347	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL
rs10861347	KIAA1033	cis	Muscle Skeletal	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105475000-105478000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr12:105476200-105478000	Flanking Active TSS	Osteobl	bone
3	chr12:105476400-105478200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:105476600-105477600	Active TSS	NHEK	skin
5	chr12:105476600-105478600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr12:105476800-105477600	Active TSS	Pancreas	Pancrea
7	chr12:105476800-105477800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
8	chr12:105476800-105477800	Flanking Active TSS	Fetal Brain Female	brain
9	chr12:105476800-105478000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
10	chr12:105476800-105478000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
11	chr12:105476800-105478000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr12:105476800-105478000	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr12:105476800-105478000	Flanking Active TSS	NH-A	brain
14	chr12:105476800-105478200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:105477000-105477600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:105477000-105477600	Flanking Active TSS	A549	lung
17	chr12:105477000-105477800	Active TSS	Colonic Mucosa	Colon
18	chr12:105477000-105478000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
19	chr12:105477000-105478000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr12:105477000-105478800	Active TSS	Brain Angular Gyrus	brain
21	chr12:105477200-105477600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:105477200-105477600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:105477200-105477600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:105477200-105477600	Flanking Active TSS	Brain Anterior Caudate	brain
25	chr12:105477200-105477600	Bivalent/Poised TSS	Fetal Stomach	stomach
26	chr12:105477200-105477600	Weak transcription	Gastric	stomach
27	chr12:105477200-105477600	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr12:105477200-105477600	Active TSS	Right Atrium	heart
29	chr12:105477200-105477600	Active TSS	Right Ventricle	heart
30	chr12:105477200-105477600	Active TSS	K562	blood
31	chr12:105477200-105477800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
32	chr12:105477200-105477800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr12:105477200-105478000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr12:105477200-105478000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:105477200-105478000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr12:105477200-105478000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr12:105477200-105478000	Flanking Active TSS	GM12878-XiMat	blood
38	chr12:105477200-105478200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
39	chr12:105477200-105478200	Active TSS	Brain Substantia Nigra	brain
40	chr12:105477200-105478200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr12:105477200-105478400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:105477200-105478400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:105477200-105478400	Active TSS	HMEC	breast
44	chr12:105477200-105478400	Active TSS	HSMMtube	muscle
45	chr12:105477200-105478600	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr12:105477200-105478600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:105477200-105478600	Active TSS	Colon Smooth Muscle	Colon
48	chr12:105477200-105478600	Active TSS	NHDF-Ad	bronchial
49	chr12:105477200-105478800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:105477200-105478800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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