Variant report

Variant	rs12728001
Chromosome Location	chr1:113076756-113076757
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113072687..113075661-chr1:113076065..113077684,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1001494	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1006298	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10745330	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776755	0.85[CEU][hapmap]
rs10776756	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10776757	0.86[CEU][hapmap]
rs10857963	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102497	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11102512	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11584092	0.85[CEU][hapmap]
rs12046208	0.85[CEU][hapmap]
rs12126277	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1994604	0.89[EUR][1000 genomes]
rs2932532	0.96[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap]
rs2932536	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs2999154	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs2999155	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs3013439	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs3013440	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs3103450	0.82[EUR][1000 genomes]
rs351372	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4839254	0.89[CEU][hapmap]
rs6537743	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666579	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6669096	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6679414	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6682737	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6691932	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6700673	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs7415820	0.96[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes]
rs7512948	0.81[EUR][1000 genomes]
rs7513716	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524494	0.82[EUR][1000 genomes]
rs7544663	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546094	0.89[EUR][1000 genomes]
rs7554345	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7554916	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs902289	0.96[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs910697	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9429486	0.86[CEU][hapmap]
rs954679	0.81[JPT][hapmap]

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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12728001	ST7L	cis	Artery Tibial	GTEx
rs12728001	ST7L	cis	multi-tissue	Pritchard
rs12728001	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs12728001	ST7L	cis	Nerve Tibial	GTEx
rs12728001	ST7L	cis	Stomach	GTEx
rs12728001	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs12728001	ST7L	cis	Adipose Subcutaneous	GTEx
rs12728001	ST7L	cis	Esophagus Muscularis	GTEx
rs12728001	ST7L	cis	Heart Left Ventricle	GTEx
rs12728001	ST7L	cis	lesional skin	skin_eQTL
rs12728001	ST7L	cis	normal skin	skin_eQTL
rs12728001	ST7L	cis	lung	GTEx
rs12728001	ST7L	cis	uninvolved skin	skin_eQTL
rs12728001	ST7L	cis	Thyroid	GTEx
rs12728001	ST7L	cis	Lymphoblastoid	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	chr1:113067000-113083800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:113067000-113117400	Weak transcription	Fetal Thymus	thymus
22	chr1:113067800-113079200	Weak transcription	Ovary	ovary
23	chr1:113067800-113083800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr1:113067800-113090200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:113068000-113089600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:113068000-113100200	Weak transcription	Fetal Heart	heart
27	chr1:113068200-113081400	Weak transcription	Fetal Lung	lung
28	chr1:113068600-113086400	Weak transcription	HUVEC	blood vessel
29	chr1:113068800-113081400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:113068800-113087000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:113069000-113081600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:113069000-113082800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:113070200-113082800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:113070200-113083800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr1:113070400-113079200	Weak transcription	HSMMtube	muscle
36	chr1:113070400-113081000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:113070400-113081400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:113070400-113086000	Weak transcription	Spleen	Spleen
39	chr1:113070400-113095400	Weak transcription	Gastric	stomach
40	chr1:113070400-113120600	Weak transcription	Right Ventricle	heart
41	chr1:113070600-113079800	Weak transcription	Left Ventricle	heart
42	chr1:113070600-113080200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr1:113070600-113080800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:113070600-113080800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr1:113070600-113081400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:113070600-113081400	Weak transcription	Lung	lung
47	chr1:113070600-113088200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:113070600-113111600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:113070600-113112400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:113070600-113112400	Weak transcription	Primary hematopoietic stem cells	blood

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