Variant report

Variant	rs12402929
Chromosome Location	chr1:113072293-113072294
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:113071935-113072377	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113070857..113072562-chr1:113074305..113076208,2	K562	blood:
2	chr1:113053258..113055489-chr1:113072240..113074967,2	MCF-7	breast:

Variant related genes	Relation type
ST7L	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10745331	0.95[CEU][hapmap]
rs10745332	0.95[CEU][hapmap]
rs11102494	0.95[EUR][1000 genomes]
rs11102508	0.84[EUR][1000 genomes]
rs11102510	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12048528	1.00[CEU][hapmap]
rs12119489	0.81[EUR][1000 genomes]
rs12125361	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs12136781	0.95[EUR][1000 genomes]
rs12137107	0.86[EUR][1000 genomes]
rs12138335	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12143068	0.86[EUR][1000 genomes]
rs12144044	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1238	1.00[CEU][hapmap]
rs12401734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12402469	0.95[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12406906	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12739994	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12750023	0.89[EUR][1000 genomes]
rs12750621	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12758377	0.86[EUR][1000 genomes]
rs17438324	0.95[EUR][1000 genomes]
rs2273369	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2279500	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2932529	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2932534	1.00[CEU][hapmap]
rs2932535	0.95[CEU][hapmap]
rs2932537	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2932538	1.00[CEU][hapmap]
rs2932539	0.93[CEU][hapmap]
rs3013441	1.00[CEU][hapmap]
rs34531155	0.86[EUR][1000 genomes]
rs35482634	0.89[EUR][1000 genomes]
rs36029940	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3762335	0.95[EUR][1000 genomes]
rs3790611	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3790612	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3795820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4240534	0.81[EUR][1000 genomes]
rs4838960	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs4838961	0.81[EUR][1000 genomes]
rs4839257	1.00[CEU][hapmap]
rs61818772	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6537740	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6537741	1.00[JPT][hapmap]
rs6537742	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs6537744	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs6537745	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs6537746	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6537747	1.00[CEU][hapmap]
rs6658555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6659677	0.95[EUR][1000 genomes]
rs6661642	0.95[EUR][1000 genomes]
rs6663922	0.93[EUR][1000 genomes]
rs6668533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671645	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6672761	0.95[EUR][1000 genomes]
rs6673930	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs6674053	0.84[EUR][1000 genomes]
rs6674068	0.85[EUR][1000 genomes]
rs6681371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6682678	0.85[CEU][hapmap]
rs6690169	0.89[EUR][1000 genomes]
rs6690292	0.94[CEU][hapmap]
rs6691025	0.83[EUR][1000 genomes]
rs6691917	0.84[EUR][1000 genomes]
rs6693880	0.90[EUR][1000 genomes]
rs6696991	0.93[EUR][1000 genomes]
rs6698030	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6701351	0.84[EUR][1000 genomes]
rs7415988	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7516421	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs7519368	0.84[ASN][1000 genomes]
rs7522110	0.95[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7527076	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs7535636	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7537789	0.92[EUR][1000 genomes]
rs7540251	0.86[EUR][1000 genomes]
rs7542820	0.88[EUR][1000 genomes]
rs7546203	0.84[EUR][1000 genomes]
rs7549547	0.95[EUR][1000 genomes]
rs7551933	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9429694	0.84[EUR][1000 genomes]
rs999923	1.00[CEU][hapmap];0.90[EUR][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	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12402929	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs12402929	ST7L	cis	lung	GTEx
rs12402929	ST7L	cis	Nerve Tibial	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113052000-113082600	Weak transcription	Brain Angular Gyrus	brain
2	chr1:113052200-113093200	Weak transcription	Brain Substantia Nigra	brain
3	chr1:113055800-113085200	Weak transcription	Thymus	Thymus
4	chr1:113058400-113086600	Weak transcription	A549	lung
5	chr1:113058800-113119400	Weak transcription	HepG2	liver
6	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
7	chr1:113061400-113081200	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:113062400-113117400	Weak transcription	Psoas Muscle	Psoas
9	chr1:113063400-113092400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:113064400-113132200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:113065000-113092400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:113065200-113114800	Weak transcription	Small Intestine	intestine
13	chr1:113065400-113114600	Weak transcription	Fetal Brain Male	brain
14	chr1:113065800-113086200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:113066000-113088800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:113066000-113114600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:113066000-113132200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:113066200-113114400	Weak transcription	Dnd41	blood
19	chr1:113066600-113081200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:113066800-113072800	Strong transcription	Fetal Muscle Leg	muscle
21	chr1:113067000-113083800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:113067000-113117400	Weak transcription	Fetal Thymus	thymus
23	chr1:113067800-113079200	Weak transcription	Ovary	ovary
24	chr1:113067800-113083800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr1:113067800-113090200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:113068000-113089600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:113068000-113100200	Weak transcription	Fetal Heart	heart
28	chr1:113068200-113081400	Weak transcription	Fetal Lung	lung
29	chr1:113068400-113074200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:113068600-113086400	Weak transcription	HUVEC	blood vessel
31	chr1:113068800-113081400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:113068800-113087000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr1:113069000-113076600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:113069000-113081600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:113069000-113082800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr1:113069400-113072600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:113069400-113072600	Enhancers	NHDF-Ad	bronchial
38	chr1:113069400-113072600	Enhancers	NHLF	lung
39	chr1:113069400-113073000	Enhancers	Osteobl	bone
40	chr1:113069800-113072600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:113070000-113073200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:113070200-113073000	Enhancers	Muscle Satellite Cultured Cells	--
43	chr1:113070200-113082800	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:113070200-113083800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:113070400-113074600	Weak transcription	Fetal Intestine Small	intestine
46	chr1:113070400-113079200	Weak transcription	HSMMtube	muscle
47	chr1:113070400-113081000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:113070400-113081400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:113070400-113086000	Weak transcription	Spleen	Spleen
50	chr1:113070400-113095400	Weak transcription	Gastric	stomach

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