Variant report

Variant	rs7542911
Chromosome Location	chr1:160984626-160984627
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:160976230..160985885-chr1:160986202..160992598,31	K562	blood:
2	chr1:160981897..160986145-chr1:160986279..160992389,24	K562	blood:
3	chr1:160983600..160986564-chr1:161134823..161137756,2	K562	blood:
4	chr1:160983895..160985741-chr1:161090954..161092534,2	MCF-7	breast:
5	chr1:160970728..160973725-chr1:160983798..160985762,2	K562	blood:
6	chr1:160963683..160965839-chr1:160983750..160985803,2	K562	blood:
7	chr1:160964339..160966592-chr1:160983829..160985803,2	K562	blood:
8	chr1:160982267..160985787-chr1:161006429..161009245,3	MCF-7	breast:
9	chr1:160982248..160985015-chr1:161041891..161043731,2	K562	blood:
10	chr1:160633216..160634752-chr1:160983475..160985241,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143224	Chromatin interaction
ENSG00000215845	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000270149	Chromatin interaction
ENSG00000158793	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10908820	0.96[ASN][1000 genomes]
rs12132502	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12758348	0.85[ASN][1000 genomes]
rs2039223	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247472	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2249933	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2250174	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2250193	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2250304	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2481076	0.94[ASN][1000 genomes]
rs2481077	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2990706	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3007155	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6427571	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6677526	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7512280	0.83[ASN][1000 genomes]
rs790055	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs790056	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7542911	TSTD1	cis	Adipose Subcutaneous	GTEx
rs7542911	TSTD1	cis	Artery Tibial	GTEx
rs7542911	TSTD1	cis	Nerve Tibial	GTEx
rs7542911	F11R	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160982400-160984800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr1:160982800-160985000	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr1:160983000-160984800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:160983600-160986400	Weak transcription	Gastric	stomach
5	chr1:160983600-160987400	Weak transcription	Fetal Brain Male	brain
6	chr1:160983600-160987800	Enhancers	Fetal Intestine Large	intestine
7	chr1:160983600-160989400	Enhancers	Placenta	Placenta
8	chr1:160983800-160986000	Weak transcription	Osteobl	bone
9	chr1:160983800-160987600	Weak transcription	Small Intestine	intestine
10	chr1:160984000-160985000	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr1:160984000-160987600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:160984200-160986200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:160984200-160986400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:160984200-160986400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:160984200-160986400	Weak transcription	Hela-S3	cervix
16	chr1:160984200-160987400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:160984200-160987600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:160984200-160987600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:160984200-160987600	Weak transcription	Psoas Muscle	Psoas
20	chr1:160984200-160987800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:160984200-160988000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:160984200-160988000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:160984200-160988200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:160984200-160989400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:160984200-160989600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:160984200-160989600	Weak transcription	Brain Anterior Caudate	brain
27	chr1:160984200-160989800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr1:160984400-160985000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:160984400-160985000	Enhancers	NHEK	skin
30	chr1:160984400-160985200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:160984400-160985400	Enhancers	Primary hematopoietic stem cells	blood
32	chr1:160984400-160986000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:160984400-160986400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:160984400-160986400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:160984400-160986400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:160984400-160986600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr1:160984400-160987000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:160984400-160987000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:160984400-160987200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr1:160984400-160987600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:160984400-160987600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:160984400-160987600	Weak transcription	Fetal Muscle Leg	muscle
43	chr1:160984400-160987600	Weak transcription	A549	lung
44	chr1:160984400-160987800	Weak transcription	Primary B cells from cord blood	blood
45	chr1:160984400-160987800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:160984400-160987800	Weak transcription	Fetal Lung	lung
47	chr1:160984400-160987800	Weak transcription	Fetal Thymus	thymus
48	chr1:160984400-160988600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:160984400-160989000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:160984400-160989400	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links