Variant report

Variant	rs40160
Chromosome Location	chr3:142695801-142695802
allele	C/T
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142695568..142698895-chr3:142718778..142721852,3	K562	blood:
2	chr3:142685155..142687473-chr3:142694018..142697111,4	K562	blood:
3	chr3:142670834..142673882-chr3:142694771..142697300,3	K562	blood:
4	chr3:142677692..142680689-chr3:142694662..142696249,2	K562	blood:
5	chr3:142687733..142690904-chr3:142694108..142697012,4	K562	blood:
6	chr3:142687639..142690486-chr3:142692515..142696128,4	K562	blood:
7	chr3:142568326..142570588-chr3:142694466..142696340,2	MCF-7	breast:
8	chr3:142692398..142697011-chr3:142719023..142723463,5	MCF-7	breast:
9	chr3:142297588..142299438-chr3:142694244..142697127,2	K562	blood:
10	chr3:142675836..142678410-chr3:142694530..142697291,2	MCF-7	breast:
11	chr3:142694373..142698058-chr3:142700090..142703022,3	K562	blood:
12	chr3:142671255..142673627-chr3:142694545..142697300,2	K562	blood:
13	chr3:142677692..142680689-chr3:142694099..142696249,3	K562	blood:
14	chr3:142680621..142683011-chr3:142695424..142697663,2	MCF-7	breast:
15	chr3:142680815..142687473-chr3:142694018..142698711,9	K562	blood:
16	chr3:142694636..142697933-chr3:142718362..142721852,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000175054	Chromatin interaction
ENSG00000241592	Chromatin interaction
ENSG00000241570	Chromatin interaction
ENSG00000163714	Chromatin interaction
ENSG00000268129	Chromatin interaction
ENSG00000188582	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs185182	0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs251484	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs251486	0.80[AMR][1000 genomes]
rs251487	0.85[JPT][hapmap]
rs251489	0.95[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs251490	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs251491	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs251492	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3101060	0.90[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs36284	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs36285	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs42381	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs668856	0.88[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	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv877563	chr3:142661350-142743889	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs40160	U2SURP	cis	lymphoblastoid	seeQTL
rs40160	SR140	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142692600-142696400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr3:142694200-142696400	Enhancers	Hela-S3	cervix
3	chr3:142694200-142699800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:142694400-142696400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:142694400-142696400	Enhancers	HepG2	liver
6	chr3:142694800-142696200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:142695000-142696200	Enhancers	Muscle Satellite Cultured Cells	--
8	chr3:142695200-142696200	Enhancers	Fetal Heart	heart
9	chr3:142695200-142696200	Enhancers	NH-A	brain
10	chr3:142695200-142696400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:142695200-142696400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr3:142695200-142696400	Enhancers	HUVEC	blood vessel
13	chr3:142695200-142696600	Flanking Active TSS	A549	lung
14	chr3:142695200-142696600	Enhancers	Osteobl	bone
15	chr3:142695400-142696000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr3:142695400-142696000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:142695400-142696000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:142695400-142696000	Enhancers	Adipose Nuclei	Adipose
19	chr3:142695400-142696000	Enhancers	Brain Substantia Nigra	brain
20	chr3:142695400-142696000	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr3:142695400-142696000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr3:142695400-142696000	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr3:142695400-142696200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:142695400-142696200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:142695400-142696200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:142695400-142696200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:142695400-142696200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:142695400-142696200	Enhancers	Stomach Mucosa	stomach
29	chr3:142695400-142696400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr3:142695400-142696400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:142695400-142696400	Flanking Active TSS	K562	blood
32	chr3:142695400-142696400	Enhancers	NHDF-Ad	bronchial
33	chr3:142695400-142696400	Enhancers	NHEK	skin
34	chr3:142695400-142696600	Enhancers	HMEC	breast
35	chr3:142695400-142700200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:142695600-142696000	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr3:142695600-142696000	Enhancers	Right Atrium	heart
38	chr3:142695600-142696200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:142695600-142696200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:142695600-142696400	Enhancers	HSMM	muscle
41	chr3:142695600-142696400	Enhancers	HSMMtube	muscle
42	chr3:142695800-142696200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr3:142695800-142696600	Enhancers	NHLF	lung
44	chr3:142695800-142700200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:142695800-142701000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:142695800-142701000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr3:142695800-142701400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:142695800-142705800	Weak transcription	Left Ventricle	heart

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