Variant report

Variant	rs2999157
Chromosome Location	chr1:113233193-113233194
allele	A/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	POLR2A	chr1:113233100-113233228	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113214618..113222446-chr1:113227384..113233520,13	K562	blood:
2	chr1:113229049..113232047-chr1:113233162..113235859,4	MCF-7	breast:

Variant related genes	Relation type
MOV10	TF binding region
ENSG00000155363	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11102512	0.81[AMR][1000 genomes]
rs12046329	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12046466	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1994604	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2932532	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932536	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2999154	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2999155	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3013431	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3013439	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3013440	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3103450	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6666579	0.81[AMR][1000 genomes]
rs6669096	0.81[AMR][1000 genomes]
rs6691932	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6700673	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7415820	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7524494	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7546094	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7554345	0.83[AMR][1000 genomes]
rs7554916	0.83[AMR][1000 genomes]
rs902289	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2999157	ST7L	cis	Thyroid	GTEx
rs2999157	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs2999157	ST7L	cis	Nerve Tibial	GTEx
rs2999157	ST7L	cis	Artery Tibial	GTEx
rs2999157	ST7L	cis	Heart Left Ventricle	GTEx
rs2999157	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs2999157	ST7L	cis	Esophagus Muscularis	GTEx
rs2999157	ST7L	cis	lung	GTEx
rs2999157	ST7L	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113218400-113234200	Weak transcription	Aorta	Aorta
2	chr1:113218600-113235000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:113218600-113235400	Weak transcription	HSMM	muscle
4	chr1:113218600-113240800	Weak transcription	Right Atrium	heart
5	chr1:113218800-113234200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:113219000-113234400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:113219000-113235400	Weak transcription	A549	lung
8	chr1:113219000-113242200	Weak transcription	NHDF-Ad	bronchial
9	chr1:113219000-113243800	Weak transcription	Fetal Brain Male	brain
10	chr1:113219400-113233200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:113220000-113234400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:113222000-113243000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:113222200-113234200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:113224800-113235000	Weak transcription	HSMMtube	muscle
15	chr1:113226000-113234200	Weak transcription	Pancreas	Pancrea
16	chr1:113228000-113234200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:113228400-113239000	Strong transcription	Fetal Intestine Small	intestine
18	chr1:113228600-113242800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:113228600-113242800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:113228800-113234200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:113229000-113235200	Weak transcription	Stomach Mucosa	stomach
22	chr1:113229000-113242200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:113229200-113237200	Weak transcription	Brain Germinal Matrix	brain
24	chr1:113229200-113248000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:113229600-113243200	Strong transcription	Dnd41	blood
26	chr1:113230200-113238000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:113230200-113239400	Strong transcription	Fetal Intestine Large	intestine
28	chr1:113230200-113239800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:113230200-113240200	Weak transcription	Fetal Heart	heart
30	chr1:113230200-113240600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:113230200-113240800	Strong transcription	Adipose Nuclei	Adipose
32	chr1:113230200-113241200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:113230200-113242600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:113230200-113243000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:113230200-113243200	Strong transcription	Primary T cells from cord blood	blood
36	chr1:113230400-113233200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:113230400-113234200	Weak transcription	GM12878-XiMat	blood
38	chr1:113230400-113240400	Strong transcription	HepG2	liver
39	chr1:113230400-113240600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr1:113230400-113241200	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:113230600-113240800	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr1:113230600-113241000	Strong transcription	Gastric	stomach
43	chr1:113230600-113241400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:113230600-113242000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:113230600-113242000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:113230600-113242200	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr1:113230600-113242600	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr1:113230800-113239800	Strong transcription	Liver	Liver
49	chr1:113230800-113240000	Strong transcription	Duodenum Mucosa	Duodenum
50	chr1:113230800-113241400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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