Variant report

Variant	rs2378908
Chromosome Location	chr17:59911765-59911766
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:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59910683..59913384-chr17:59939792..59942548,3	K562	blood:
2	chr17:59655679..59662005-chr17:59908866..59914904,7	MCF-7	breast:
3	chr17:59731140..59732709-chr17:59911539..59913325,2	MCF-7	breast:
4	chr17:59485300..59495746-chr17:59906301..59920408,36	MCF-7	breast:
5	chr17:59910379..59913191-chr20:55840905..55842776,2	MCF-7	breast:
6	chr17:59524968..59526550-chr17:59911521..59913626,2	MCF-7	breast:
7	chr17:59486004..59494842-chr17:59908668..59916445,28	MCF-7	breast:
8	chr17:59708854..59715538-chr17:59908174..59913185,10	MCF-7	breast:
9	chr17:59909807..59912153-chr20:49407963..49409870,2	MCF-7	breast:
10	chr17:59900956..59905139-chr17:59907699..59912131,8	MCF-7	breast:
11	chr17:59497346..59499681-chr17:59911621..59914856,3	MCF-7	breast:
12	chr17:59784025..59787168-chr17:59909031..59912201,3	MCF-7	breast:
13	chr17:59711578..59716020-chr17:59910074..59916640,13	MCF-7	breast:
14	chr17:59476759..59479299-chr17:59911039..59913181,3	MCF-7	breast:
15	chr17:59911219..59913384-chr17:59939792..59942139,2	K562	blood:
16	chr17:59910616..59917582-chr17:59936691..59943102,15	MCF-7	breast:
17	chr17:59911641..59916436-chr20:55839275..55842881,5	MCF-7	breast:
18	chr17:59908956..59912100-chr20:60640245..60642593,4	MCF-7	breast:
19	chr17:59890246..59897512-chr17:59906301..59911865,9	MCF-7	breast:
20	chr17:59686543..59688789-chr17:59909951..59912195,2	MCF-7	breast:
21	chr17:59802918..59807240-chr17:59907754..59912579,5	MCF-7	breast:
22	chr17:59833992..59836586-chr17:59910616..59913241,3	MCF-7	breast:
23	chr17:59866718..59868702-chr17:59911534..59913402,2	MCF-7	breast:
24	chr17:59716212..59718286-chr17:59910672..59913286,2	MCF-7	breast:
25	chr17:59910605..59912694-chr20:55836823..55839521,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000136492	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000130699	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000267280	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10512492	0.88[GIH][hapmap]
rs11079457	0.91[ASN][1000 genomes]
rs12451910	0.83[GIH][hapmap];0.94[TSI][hapmap]
rs12453644	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12601269	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12604037	0.83[GIH][hapmap];0.94[TSI][hapmap]
rs16945692	0.88[GIH][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs16945759	0.88[GIH][hapmap];0.88[TSI][hapmap]
rs2271576	0.88[GIH][hapmap];0.94[TSI][hapmap]
rs2278812	0.87[GIH][hapmap];0.85[MEX][hapmap]
rs3744434	0.88[GIH][hapmap];0.94[TSI][hapmap]
rs4968408	0.88[GIH][hapmap];0.94[TSI][hapmap]
rs4968451	0.84[CHD][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs4968452	0.82[EUR][1000 genomes]
rs4968460	0.88[GIH][hapmap];0.94[TSI][hapmap]
rs4988344	0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs61169879	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7218724	0.88[GIH][hapmap];0.94[TSI][hapmap]
rs7221089	0.88[GIH][hapmap]
rs8066964	0.88[GIH][hapmap]
rs8080599	0.88[GIH][hapmap];0.94[TSI][hapmap]
rs8081917	0.88[GIH][hapmap];0.94[TSI][hapmap]
rs9630735	0.84[EUR][1000 genomes]
rs9630736	0.88[GIH][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv908673	chr17:59767501-59926645	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
3	nsv575841	chr17:59812748-59914681	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
4	nsv575842	chr17:59812748-59927307	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
5	nsv908675	chr17:59835864-59937286	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
6	nsv575843	chr17:59869081-59935723	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2378908	MED13	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59863600-59925000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr17:59870400-59933400	Weak transcription	Fetal Intestine Large	intestine
3	chr17:59884200-59933200	Weak transcription	K562	blood
4	chr17:59894000-59922400	Weak transcription	Osteobl	bone
5	chr17:59894800-59922000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr17:59898200-59912000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr17:59898800-59914400	Weak transcription	Primary B cells from cord blood	blood
8	chr17:59898800-59920800	Weak transcription	Thymus	Thymus
9	chr17:59898800-59939600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr17:59898800-59939800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr17:59899200-59919000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr17:59899400-59920600	Weak transcription	Fetal Thymus	thymus
13	chr17:59899400-59924200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr17:59904200-59927000	Weak transcription	Fetal Kidney	kidney
15	chr17:59904800-59933200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr17:59905000-59912600	Strong transcription	Dnd41	blood
17	chr17:59905400-59923800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr17:59905400-59931400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr17:59905600-59923800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr17:59905800-59919000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr17:59905800-59920600	Weak transcription	Primary hematopoietic stem cells	blood
22	chr17:59905800-59923600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr17:59905800-59939000	Weak transcription	Primary T cells from cord blood	blood
24	chr17:59906000-59914000	Weak transcription	HepG2	liver
25	chr17:59906000-59919200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr17:59906200-59921400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr17:59906200-59940200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr17:59906400-59912000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr17:59906400-59919000	Weak transcription	GM12878-XiMat	blood
30	chr17:59906400-59919200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr17:59907800-59920200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:59909600-59913600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr17:59910000-59921200	Weak transcription	Fetal Muscle Leg	muscle
34	chr17:59910200-59912000	Enhancers	A549	lung
35	chr17:59910200-59918800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr17:59910400-59912400	Enhancers	NHEK	skin
37	chr17:59910600-59911800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr17:59910600-59912400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr17:59910600-59912400	Enhancers	Hela-S3	cervix
40	chr17:59910600-59912400	Enhancers	HMEC	breast
41	chr17:59910600-59914400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr17:59911000-59911800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr17:59911000-59911800	Enhancers	NH-A	brain
44	chr17:59911000-59912000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr17:59911000-59912200	Enhancers	NHLF	lung
46	chr17:59911000-59912400	Enhancers	NHDF-Ad	bronchial
47	chr17:59911000-59914600	Enhancers	Fetal Lung	lung
48	chr17:59911200-59911800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr17:59911200-59912000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr17:59911200-59912000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links