Variant report

Variant	rs10746010
Chromosome Location	chr12:105477783-105477784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105476762..105478986-chr12:105499431..105503042,4	K562	blood:
2	chr12:105476808..105479481-chr12:105501524..105503382,3	K562	blood:
3	chr12:105477772..105479851-chr12:105501425..105505225,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136051	Chromatin interaction
ENSG00000257999	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10778367	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778368	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778369	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1196742	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196745	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196748	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196749	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196753	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196754	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196756	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196759	1.00[ASN][1000 genomes]
rs1196760	1.00[ASN][1000 genomes]
rs1196764	0.89[EUR][1000 genomes]
rs1196765	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196770	0.83[EUR][1000 genomes]
rs1196772	0.83[EUR][1000 genomes]
rs1196777	0.82[EUR][1000 genomes]
rs1196798	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196800	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196801	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196805	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196806	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196807	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196808	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196811	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1196813	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196817	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196819	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196820	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196823	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196825	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196831	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196833	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196839	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196841	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196842	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196844	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196848	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196851	0.88[EUR][1000 genomes]
rs1196853	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196857	1.00[ASN][1000 genomes]
rs1196859	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196861	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196862	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196864	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196869	0.89[EUR][1000 genomes]
rs1196871	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196872	0.88[EUR][1000 genomes]
rs1196873	0.89[EUR][1000 genomes]
rs1196874	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196881	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196884	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196885	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1206559	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1209308	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211276	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1211277	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345096	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1621553	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1663564	1.00[ASN][1000 genomes]
rs1663565	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732370	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166142	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246243	0.82[EUR][1000 genomes]
rs2257156	0.88[EUR][1000 genomes]
rs2374449	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2440692	0.88[EUR][1000 genomes]
rs2440714	0.91[EUR][1000 genomes]
rs2440715	1.00[ASN][1000 genomes]
rs2440718	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464173	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464175	0.89[EUR][1000 genomes]
rs2464181	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464182	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4356312	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356313	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4372534	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4390426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964122	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964331	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6539183	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6539186	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6539187	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539188	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7132040	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132624	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7132855	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71441895	0.83[EUR][1000 genomes]
rs7299701	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7302854	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7303961	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7963877	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs935240	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935241	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935242	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935244	0.83[EUR][1000 genomes]
rs935246	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935248	0.89[EUR][1000 genomes]
rs935249	0.88[EUR][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10746010	ALDH1L2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 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	chr12:105476600-105478600	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr12:105476800-105477800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
6	chr12:105476800-105477800	Flanking Active TSS	Fetal Brain Female	brain
7	chr12:105476800-105478000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
8	chr12:105476800-105478000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
9	chr12:105476800-105478000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr12:105476800-105478000	Flanking Active TSS	Stomach Smooth Muscle	stomach
11	chr12:105476800-105478000	Flanking Active TSS	NH-A	brain
12	chr12:105476800-105478200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:105477000-105477800	Active TSS	Colonic Mucosa	Colon
14	chr12:105477000-105478000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
15	chr12:105477000-105478000	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr12:105477000-105478800	Active TSS	Brain Angular Gyrus	brain
17	chr12:105477200-105477800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
18	chr12:105477200-105477800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
19	chr12:105477200-105478000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
20	chr12:105477200-105478000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:105477200-105478000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr12:105477200-105478000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr12:105477200-105478000	Flanking Active TSS	GM12878-XiMat	blood
24	chr12:105477200-105478200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr12:105477200-105478200	Active TSS	Brain Substantia Nigra	brain
26	chr12:105477200-105478200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr12:105477200-105478400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:105477200-105478400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:105477200-105478400	Active TSS	HMEC	breast
30	chr12:105477200-105478400	Active TSS	HSMMtube	muscle
31	chr12:105477200-105478600	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr12:105477200-105478600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:105477200-105478600	Active TSS	Colon Smooth Muscle	Colon
34	chr12:105477200-105478600	Active TSS	NHDF-Ad	bronchial
35	chr12:105477200-105478800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:105477200-105478800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:105477200-105478800	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr12:105477200-105478800	Active TSS	HSMM	muscle
39	chr12:105477200-105479000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr12:105477400-105477800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:105477400-105477800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:105477400-105477800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
43	chr12:105477400-105477800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
44	chr12:105477400-105477800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
45	chr12:105477400-105477800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:105477400-105477800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
47	chr12:105477400-105477800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
48	chr12:105477400-105477800	Flanking Bivalent TSS/Enh	Placenta	Placenta
49	chr12:105477400-105477800	Flanking Active TSS	Ovary	ovary
50	chr12:105477400-105478000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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