Variant report

Variant	rs12758377
Chromosome Location	chr1:113137221-113137222
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113133172..113139000-chr1:113157141..113162123,6	K562	blood:
2	chr1:113134544..113137482-chr1:113243651..113245216,2	MCF-7	breast:
3	chr1:113135812..113137373-chr1:113160331..113162478,2	MCF-7	breast:
4	chr1:113131312..113132892-chr1:113136156..113138926,2	K562	blood:
5	chr1:113137197..113139930-chr1:113155526..113159416,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116489	Chromatin interaction
ENSG00000007341	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10745332	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10857969	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11102494	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11102508	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102510	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11102517	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12048528	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12118370	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12119489	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125361	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12126494	0.81[EUR][1000 genomes]
rs12136781	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12137107	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138335	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12143068	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1238	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12401734	0.86[EUR][1000 genomes]
rs12402469	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12402929	0.86[EUR][1000 genomes]
rs12406906	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739994	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12750023	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12750621	0.82[EUR][1000 genomes]
rs17438324	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2273369	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932529	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2932534	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2932535	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2932538	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2932539	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3013441	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34531155	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35482634	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36029940	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3762335	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3790611	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3790612	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3795820	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4240534	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4838960	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4838961	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4839257	0.85[ASN][1000 genomes]
rs61818772	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61818800	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537740	0.88[EUR][1000 genomes]
rs6537744	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6537745	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537746	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6537747	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6658555	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6659677	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6661642	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6663922	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6668533	0.85[EUR][1000 genomes]
rs6671645	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672761	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6673930	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674053	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674068	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681371	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6682678	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6690169	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690292	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6691025	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6691917	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693880	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6696991	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6698030	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6701351	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415988	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7516421	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7519368	0.89[EUR][1000 genomes]
rs7522110	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7527076	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7535636	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7537789	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7540251	0.82[EUR][1000 genomes]
rs7542820	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546203	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7549547	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7551933	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7552692	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9429694	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9662162	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs999923	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12758377	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs12758377	ST7L	cis	lung	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113092000-113151200	Weak transcription	Colonic Mucosa	Colon
2	chr1:113109000-113160000	Weak transcription	Gastric	stomach
3	chr1:113109200-113152600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:113111800-113138800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:113115400-113154200	Weak transcription	Esophagus	oesophagus
6	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
7	chr1:113116400-113160000	Weak transcription	Spleen	Spleen
8	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:113118800-113160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:113119000-113138400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:113121000-113148400	Weak transcription	Stomach Mucosa	stomach
12	chr1:113124600-113148400	Weak transcription	NHLF	lung
13	chr1:113125000-113142000	Weak transcription	Hela-S3	cervix
14	chr1:113126800-113143400	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:113128000-113148400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:113129000-113147200	Strong transcription	HSMM	muscle
17	chr1:113129600-113159000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:113130200-113141000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:113131200-113137400	Strong transcription	Placenta	Placenta
20	chr1:113131400-113160000	Weak transcription	Fetal Heart	heart
21	chr1:113131600-113147200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:113132600-113139800	Weak transcription	NHEK	skin
23	chr1:113132600-113148400	Weak transcription	Lung	lung
24	chr1:113132600-113148400	Weak transcription	Pancreas	Pancrea
25	chr1:113132600-113148400	Weak transcription	Thymus	Thymus
26	chr1:113132600-113152400	Weak transcription	Psoas Muscle	Psoas
27	chr1:113132600-113154800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:113132600-113159800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:113132800-113139400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:113132800-113140000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:113132800-113143400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:113132800-113144200	Weak transcription	Right Ventricle	heart
33	chr1:113132800-113145400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:113133000-113137600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:113133000-113137600	Weak transcription	Fetal Intestine Small	intestine
36	chr1:113133000-113137800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:113133000-113138000	Weak transcription	Left Ventricle	heart
38	chr1:113133000-113138200	Weak transcription	Fetal Stomach	stomach
39	chr1:113133000-113138800	Weak transcription	Primary T cells from cord blood	blood
40	chr1:113133000-113138800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:113133000-113139000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:113133000-113139400	Weak transcription	Brain Substantia Nigra	brain
43	chr1:113133000-113139600	Weak transcription	HMEC	breast
44	chr1:113133000-113142000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:113133000-113142600	Weak transcription	Aorta	Aorta
46	chr1:113133000-113143400	Weak transcription	HepG2	liver
47	chr1:113133000-113143800	Weak transcription	Ovary	ovary
48	chr1:113133000-113148400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:113133000-113148400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr1:113133000-113148600	Weak transcription	HSMMtube	muscle

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