Variant report

Variant	rs12126494
Chromosome Location	chr1:113228623-113228624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113214618..113222446-chr1:113227384..113233520,13	K562	blood:
2	chr1:113217617..113223835-chr1:113226384..113230990,8	MCF-7	breast:
3	chr1:113226289..113228900-chr1:113228989..113230932,2	MCF-7	breast:
4	chr1:113214399..113219266-chr1:113227839..113232151,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155363	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10745332	0.94[EUR][1000 genomes]
rs10857969	0.90[EUR][1000 genomes]
rs11102510	0.83[EUR][1000 genomes]
rs12048528	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12125361	0.83[EUR][1000 genomes]
rs12137107	0.81[EUR][1000 genomes]
rs12138335	0.81[EUR][1000 genomes]
rs12143068	0.81[EUR][1000 genomes]
rs1238	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12739994	0.81[EUR][1000 genomes]
rs12750621	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12758377	0.81[EUR][1000 genomes]
rs2279500	1.00[ASN][1000 genomes]
rs2932529	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2932534	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2932535	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2932537	1.00[ASN][1000 genomes]
rs2932538	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2932539	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2999159	1.00[ASN][1000 genomes]
rs3013433	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3013441	0.94[EUR][1000 genomes]
rs34531155	0.81[EUR][1000 genomes]
rs35221527	0.95[ASN][1000 genomes]
rs3795820	0.85[EUR][1000 genomes]
rs4240534	0.84[EUR][1000 genomes]
rs4838960	0.82[EUR][1000 genomes]
rs4838961	0.84[EUR][1000 genomes]
rs4839257	0.96[EUR][1000 genomes]
rs6537745	0.80[EUR][1000 genomes]
rs6537746	0.85[EUR][1000 genomes]
rs6537747	0.83[EUR][1000 genomes]
rs6674053	0.81[EUR][1000 genomes]
rs6674068	0.83[EUR][1000 genomes]
rs6682678	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6690292	0.90[EUR][1000 genomes]
rs6691025	0.85[EUR][1000 genomes]
rs6698030	0.81[EUR][1000 genomes]
rs7415988	0.84[EUR][1000 genomes]
rs7512984	0.88[EUR][1000 genomes]
rs7527076	0.84[EUR][1000 genomes]
rs7546203	0.84[EUR][1000 genomes]
rs9429694	0.84[EUR][1000 genomes]
rs9662162	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
5	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12126494	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs12126494	ST7L	cis	lung	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113218400-113230200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:113218400-113230400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:113218400-113234200	Weak transcription	Aorta	Aorta
4	chr1:113218600-113230200	Weak transcription	Lung	lung
5	chr1:113218600-113232200	Weak transcription	Ovary	ovary
6	chr1:113218600-113235000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:113218600-113235400	Weak transcription	HSMM	muscle
8	chr1:113218600-113240800	Weak transcription	Right Atrium	heart
9	chr1:113218800-113229200	Weak transcription	Placenta	Placenta
10	chr1:113218800-113230000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:113218800-113230000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:113218800-113230200	Weak transcription	Left Ventricle	heart
13	chr1:113218800-113230400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:113218800-113230600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:113218800-113232200	Weak transcription	Colonic Mucosa	Colon
16	chr1:113218800-113232400	Weak transcription	Brain Substantia Nigra	brain
17	chr1:113218800-113234200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:113219000-113228800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:113219000-113228800	Weak transcription	Osteobl	bone
20	chr1:113219000-113230200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:113219000-113230600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr1:113219000-113231400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:113219000-113232000	Weak transcription	Hela-S3	cervix
24	chr1:113219000-113232200	Weak transcription	Small Intestine	intestine
25	chr1:113219000-113232400	Weak transcription	Brain Anterior Caudate	brain
26	chr1:113219000-113234400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:113219000-113235400	Weak transcription	A549	lung
28	chr1:113219000-113242200	Weak transcription	NHDF-Ad	bronchial
29	chr1:113219000-113243800	Weak transcription	Fetal Brain Male	brain
30	chr1:113219200-113228800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:113219200-113228800	Weak transcription	HMEC	breast
32	chr1:113219200-113230800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:113219200-113230800	Weak transcription	NHLF	lung
34	chr1:113219200-113232200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:113219200-113232400	Weak transcription	HUVEC	blood vessel
36	chr1:113219400-113229000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:113219400-113230200	Weak transcription	Primary T cells from cord blood	blood
38	chr1:113219400-113230200	Weak transcription	Adipose Nuclei	Adipose
39	chr1:113219400-113230400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:113219400-113230400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:113219400-113230600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:113219400-113231400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:113219400-113232600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:113219400-113233200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:113219600-113229200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:113219600-113229600	Weak transcription	Fetal Thymus	thymus
47	chr1:113219600-113230600	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr1:113219600-113230600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:113219600-113230600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:113219600-113231000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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