Variant report

Variant	rs62067380
Chromosome Location	chr17:46000406-46000407
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45973963..45975508-chr17:45999326..46001270,2	MCF-7	breast:
2	chr17:45973265..45977043-chr17:45998491..46003792,7	MCF-7	breast:
3	chr17:45999369..46002049-chr17:46009098..46012075,3	MCF-7	breast:
4	chr17:46000022..46002269-chr17:46003613..46007289,3	MCF-7	breast:
5	chr17:45991986..45994660-chr17:45998582..46001397,3	K562	blood:
6	chr17:45990771..45994045-chr17:45997430..46001241,5	MCF-7	breast:
7	chr17:45981911..45983503-chr17:45998627..46000923,2	K562	blood:
8	chr17:45989573..45991691-chr17:45999240..46001944,2	K562	blood:
9	chr17:45999533..46002331-chr17:46009358..46011898,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000167182	Chromatin interaction
ENSG00000266601	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11871969	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4794318	0.84[AFR][1000 genomes]
rs60123006	0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1062503	chr17:45977445-46021384	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	nsv2072	chr17:45998637-46019626	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62067380	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs62067380	SCRN2	cis	Skin Sun Exposed Lower leg	GTEx
rs62067380	SCRN2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45975800-46000600	Weak transcription	Hela-S3	cervix
2	chr17:45980200-46001800	Weak transcription	K562	blood
3	chr17:45980200-46002400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:45980200-46006400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr17:45982400-46000600	Weak transcription	Stomach Mucosa	stomach
6	chr17:45983000-46001000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr17:45983000-46004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr17:45983200-46001200	Weak transcription	A549	lung
9	chr17:45983200-46018200	Weak transcription	Fetal Brain Male	brain
10	chr17:45983400-46000600	Weak transcription	NHDF-Ad	bronchial
11	chr17:45984200-46000600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr17:45985600-46000600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr17:45988400-46000600	Weak transcription	HSMM	muscle
14	chr17:45991800-46006400	Strong transcription	Fetal Stomach	stomach
15	chr17:45992400-46008400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr17:45993600-46000600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr17:45993800-46017400	Weak transcription	Psoas Muscle	Psoas
18	chr17:45994000-46000600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr17:45994000-46013200	Weak transcription	Fetal Heart	heart
20	chr17:45994200-46006000	Strong transcription	Fetal Muscle Trunk	muscle
21	chr17:45994400-46002400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr17:45994400-46006000	Strong transcription	Fetal Muscle Leg	muscle
23	chr17:45994800-46000600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr17:45994800-46002400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:45995200-46000600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr17:45995800-46000600	Weak transcription	HMEC	breast
27	chr17:45995800-46000800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr17:45995800-46012200	Weak transcription	HUVEC	blood vessel
29	chr17:45996000-46000600	Weak transcription	NHEK	skin
30	chr17:45996000-46000600	Weak transcription	Osteobl	bone
31	chr17:45996000-46008200	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr17:45996200-46008200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr17:45996200-46012600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr17:45996600-46005000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr17:45996600-46008400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr17:45997400-46008200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr17:45997600-46000600	Weak transcription	HepG2	liver
38	chr17:45997600-46006200	Strong transcription	Fetal Intestine Small	intestine
39	chr17:45998000-46008200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr17:45998000-46009400	Strong transcription	Fetal Thymus	thymus
41	chr17:45998200-46001400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr17:45998200-46008000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr17:45998200-46008200	Strong transcription	Dnd41	blood
44	chr17:45998200-46008400	Strong transcription	Primary B cells from peripheral blood	blood
45	chr17:45998200-46008400	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr17:45998200-46011000	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr17:45998400-46003200	Strong transcription	GM12878-XiMat	blood
48	chr17:45998400-46005000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr17:45998400-46005200	Strong transcription	Fetal Lung	lung
50	chr17:45998400-46006000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links