Variant report

Variant	rs12119489
Chromosome Location	chr1:113128286-113128287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10745332	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10857969	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11102494	0.85[EUR][1000 genomes]
rs11102508	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102510	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11102517	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12048528	0.83[ASN][1000 genomes]
rs12118370	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12125361	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12136781	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12137107	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138335	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12143068	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1238	0.85[ASN][1000 genomes]
rs12401734	0.81[EUR][1000 genomes]
rs12402469	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12402929	0.81[EUR][1000 genomes]
rs12406906	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739994	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12750023	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758377	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17438324	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2273369	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932529	0.82[AMR][1000 genomes]
rs2932534	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2932535	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2932538	0.86[ASN][1000 genomes]
rs2932539	0.86[ASN][1000 genomes]
rs3013441	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34531155	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35482634	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36029940	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3762335	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3790611	0.89[ASN][1000 genomes]
rs3790612	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3795820	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4240534	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4838960	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4838961	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4839257	0.85[ASN][1000 genomes]
rs61818772	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61818800	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537740	0.82[EUR][1000 genomes]
rs6537744	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6537745	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6537746	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6537747	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6658555	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6659677	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6661642	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6663922	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6671645	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672761	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6673930	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674053	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674068	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6681371	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6682678	0.85[ASN][1000 genomes]
rs6690169	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690292	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6691025	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6691917	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693880	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6696991	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6698030	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6701351	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7415988	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7516421	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7519368	0.83[EUR][1000 genomes]
rs7522110	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7527076	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7535636	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7537789	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7540251	0.81[EUR][1000 genomes]
rs7542820	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546203	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7549547	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7551933	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7552692	0.87[ASN][1000 genomes]
rs9429694	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9662162	0.84[ASN][1000 genomes]
rs999923	0.88[AMR][1000 genomes];0.85[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12119489	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs12119489	ST7L	cis	lung	GTEx
rs12119489	ST7L	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
2	chr1:113064400-113132200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:113066000-113132200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:113070600-113132400	Weak transcription	Aorta	Aorta
5	chr1:113081200-113132200	Weak transcription	Primary B cells from cord blood	blood
6	chr1:113081400-113132400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:113081800-113132200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr1:113084000-113131400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:113084800-113137000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:113088400-113132200	Weak transcription	HMEC	breast
11	chr1:113092000-113151200	Weak transcription	Colonic Mucosa	Colon
12	chr1:113105400-113129800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:113109000-113160000	Weak transcription	Gastric	stomach
14	chr1:113109200-113152600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:113111000-113131000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:113111800-113138800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:113112600-113131800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:113113200-113132400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:113115000-113128800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:113115200-113130200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:113115400-113154200	Weak transcription	Esophagus	oesophagus
22	chr1:113115800-113130800	Weak transcription	Fetal Brain Male	brain
23	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
24	chr1:113116000-113132400	Weak transcription	Thymus	Thymus
25	chr1:113116400-113160000	Weak transcription	Spleen	Spleen
26	chr1:113117000-113132200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:113117200-113132200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:113117200-113132400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:113117400-113132200	Weak transcription	GM12878-XiMat	blood
30	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:113118400-113132400	Weak transcription	Brain Substantia Nigra	brain
32	chr1:113118600-113132200	Weak transcription	A549	lung
33	chr1:113118800-113131200	Weak transcription	Brain Angular Gyrus	brain
34	chr1:113118800-113132200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:113118800-113160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:113119000-113131000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:113119000-113132200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:113119000-113132200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:113119000-113132400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:113119000-113138400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr1:113119200-113131800	Weak transcription	Lung	lung
42	chr1:113119200-113132400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:113119200-113132400	Weak transcription	Fetal Thymus	thymus
44	chr1:113121000-113130600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:113121000-113130800	Weak transcription	Fetal Heart	heart
46	chr1:113121000-113132000	Weak transcription	Right Ventricle	heart
47	chr1:113121000-113132000	Weak transcription	HSMMtube	muscle
48	chr1:113121000-113132000	Weak transcription	HUVEC	blood vessel
49	chr1:113121000-113132200	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr1:113121000-113132200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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