Variant report

Variant	rs2075159
Chromosome Location	chr16:11944709-11944710
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	SIN3AK20	chr16:11944586-11946428	MCF-7	breast:	n/a	n/a
2	RPC155	chr16:11944490-11945048	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr16:11944546-11946268	HepG2	liver:	n/a	n/a
4	SIN3A	chr16:11944524-11946064	GM12878	blood:	n/a	chr16:11945075-11945089
5	POLR2A	chr16:11944693-11946146	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr16:11944457-11946650	MCF10A-Er-Src	breast:	n/a	n/a
7	MXI1	chr16:11943880-11946788	SK-N-SH	brain:	n/a	chr16:11945100-11945109 chr16:11945769-11945778
8	POLR2A	chr16:11944692-11945846	H1-hESC	embryonic stem cell:	n/a	n/a
9	YY1	chr16:11944635-11946287	HepG2	liver:	n/a	n/a
10	MYC	chr16:11944424-11946597	K562	blood:	n/a	chr16:11945727-11945736 chr16:11945935-11945945 chr16:11945456-11945466
11	POLR2A	chr16:11944494-11946695	K562	blood:	n/a	n/a
12	MXI1	chr16:11943898-11946813	IMR90	lung:	n/a	chr16:11945100-11945109 chr16:11945769-11945778
13	SREBP2	chr16:11944607-11946420	GM12878	blood:	n/a	n/a
14	HCFC1	chr16:11944245-11946232	Hela-S3	cervix:	n/a	n/a
15	SIN3A	chr16:11944576-11946230	H1-hESC	embryonic stem cell:	n/a	chr16:11945075-11945089
16	GTF3C2	chr16:11944447-11944904	Hela-S3	cervix:	n/a	n/a
17	YY1	chr16:11944624-11945938	SK-N-SH	brain:	n/a	n/a
18	REST	chr16:11944704-11946204	H1-neurons	neurons:	n/a	chr16:11945074-11945094 chr16:11944851-11944859
19	POLR2A	chr16:11944703-11946371	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:11944315..11946480-chr16:12008232..12011350,3	K562	blood:
2	chr16:11891005..11893828-chr16:11944573..11948679,5	MCF-7	breast:
3	chr16:11889197..11895021-chr16:11943442..11946851,6	K562	blood:
4	chr11:65625292..65625927-chr16:11944475..11945055,2	HCT-116	colon:
5	chr16:11941713..11946689-chr16:12006948..12011249,6	MCF-7	breast:
6	chr16:11940299..11942446-chr16:11943353..11945680,3	K562	blood:
7	chr16:11922509..11925081-chr16:11942890..11945014,2	MCF-7	breast:
8	chr16:11889713..11895021-chr16:11941964..11945200,5	K562	blood:
9	chr16:11942158..11945019-chr16:12007276..12009748,2	K562	blood:
10	chr16:11936442..11940721-chr16:11941344..11946764,13	K562	blood:
11	chr16:11943912..11945965-chr16:12008319..12011491,4	MCF-7	breast:
12	chr16:11834777..11836567-chr16:11943909..11945629,3	K562	blood:
13	chr16:11874839..11876842-chr16:11943852..11946760,2	K562	blood:
14	chr16:11874200..11876842-chr16:11943852..11945564,2	K562	blood:

Variant related genes	Relation type
RSL1D1	TF binding region
ENSG00000263307	TF binding region
ENSG00000153066	Chromatin interaction
ENSG00000262420	Chromatin interaction
ENSG00000171490	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000266163	Chromatin interaction
ENSG00000122299	Chromatin interaction
ENSG00000262117	Chromatin interaction
ENSG00000103342	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10744977	0.92[ASN][1000 genomes]
rs11075022	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11646545	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11647818	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11649405	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12925740	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs153025	0.86[EUR][1000 genomes]
rs154148	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs171656	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2075158	0.81[EUR][1000 genomes]
rs251723	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28279	0.87[EUR][1000 genomes]
rs33631	0.81[EUR][1000 genomes]
rs33637	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs33640	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs33643	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs33645	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs33647	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs33649	0.85[EUR][1000 genomes]
rs33651	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs33652	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs33653	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs33655	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs33660	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35153773	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs40311	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4511557	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs718081	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7185589	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7193470	0.86[ASN][1000 genomes]
rs7196913	0.92[ASN][1000 genomes]
rs7197111	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7198817	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7202234	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8046617	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8047726	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8061189	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482288	chr16:11776491-11946429	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1043909	chr16:11839910-12007435	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2075159	GSPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:11943200-11944800	Weak transcription	Spleen	Spleen
2	chr16:11943800-11944800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr16:11943800-11945000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr16:11943800-11946400	Active TSS	HMEC	breast
5	chr16:11943800-11946600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr16:11944000-11944800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr16:11944000-11945200	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr16:11944000-11946200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
9	chr16:11944000-11946400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr16:11944000-11946400	Active TSS	Fetal Brain Female	brain
11	chr16:11944000-11946400	Active TSS	NHLF	lung
12	chr16:11944000-11946600	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr16:11944000-11946600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr16:11944000-11946600	Active TSS	Psoas Muscle	Psoas
15	chr16:11944200-11944800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr16:11944200-11944800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr16:11944200-11944800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr16:11944200-11944800	Flanking Active TSS	Fetal Thymus	thymus
19	chr16:11944200-11945000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr16:11944200-11945000	Active TSS	Right Atrium	heart
21	chr16:11944200-11945200	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr16:11944200-11945200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr16:11944200-11945800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr16:11944200-11945800	Active TSS	Fetal Muscle Trunk	muscle
25	chr16:11944200-11945800	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr16:11944200-11946200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr16:11944200-11946200	Active TSS	H9 Cell Line	embryonic stem cell
28	chr16:11944200-11946400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr16:11944200-11946400	Active TSS	H1 Cell Line	embryonic stem cell
30	chr16:11944200-11946400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr16:11944200-11946400	Active TSS	Ovary	ovary
32	chr16:11944200-11946600	Active TSS	HSMM	muscle
33	chr16:11944200-11946800	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr16:11944200-11946800	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr16:11944200-11946800	Active TSS	GM12878-XiMat	blood
36	chr16:11944200-11947200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr16:11944400-11944800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr16:11944400-11944800	Flanking Active TSS	Stomach Smooth Muscle	stomach
39	chr16:11944400-11945000	Active TSS	Brain Germinal Matrix	brain
40	chr16:11944400-11945200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr16:11944400-11945200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr16:11944400-11945600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr16:11944400-11945800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr16:11944400-11945800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr16:11944400-11946000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr16:11944400-11946000	Active TSS	Lung	lung
47	chr16:11944400-11946200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr16:11944400-11946200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr16:11944400-11946200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr16:11944400-11946200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links