Variant report

Variant	rs12188129
Chromosome Location	chr5:40781559-40781560
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:40767281..40769776-chr5:40780644..40782571,2	K562	blood:
2	chr5:40780330..40783240-chr5:40783326..40786085,3	K562	blood:
3	chr5:40772685..40774717-chr5:40780854..40782861,2	MCF-7	breast:
4	chr5:39697407..39700282-chr5:40780176..40782175,2	MCF-7	breast:
5	chr5:40776129..40777885-chr5:40780010..40782905,2	MCF-7	breast:
6	chr5:40776304..40779172-chr5:40780359..40783099,2	MCF-7	breast:
7	chr5:40779894..40785582-chr5:40828129..40833355,6	K562	blood:
8	chr5:40764714..40766607-chr5:40780261..40782554,2	K562	blood:
9	chr5:40772521..40774883-chr5:40778723..40781622,3	K562	blood:
10	chr5:40773032..40774883-chr5:40778723..40781622,2	K562	blood:
11	chr5:40779717..40782233-chr5:40797483..40800028,2	MCF-7	breast:
12	chr5:40778589..40781833-chr5:40798494..40800242,3	K562	blood:
13	chr5:40779573..40785197-chr5:40796111..40799754,6	MCF-7	breast:
14	chr5:40780546..40782142-chr5:40840625..40843582,2	K562	blood:
15	chr5:40780330..40782548-chr5:40784547..40786085,2	K562	blood:
16	chr5:40776383..40778845-chr5:40780186..40782219,2	K562	blood:
17	chr5:40780906..40782873-chr5:40789794..40792665,2	MCF-7	breast:
18	chr5:40755376..40758160-chr5:40779658..40781584,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000132357	Chromatin interaction
ENSG00000113638	Chromatin interaction
ENSG00000132356	Chromatin interaction
ENSG00000145592	Chromatin interaction
ENSG00000212296	Chromatin interaction
ENSG00000212567	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10064650	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap]
rs1070444	1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap]
rs11740266	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743132	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11743196	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11745121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748743	0.93[EUR][1000 genomes]
rs11749180	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11749437	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186450	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs12188981	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35999176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62356509	1.00[ASN][1000 genomes]
rs62356512	1.00[ASN][1000 genomes]
rs62356519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357568	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62357569	0.83[AMR][1000 genomes]
rs62357570	0.83[AMR][1000 genomes]
rs62357571	0.83[AMR][1000 genomes]
rs704034	1.00[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881377	chr5:40753877-40810426	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12188129	GDNF	cis	cerebellum	SCAN
rs12188129	ZNF131	cis	cerebellum	SCAN
rs12188129	NVL	trans	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40756200-40797200	Weak transcription	Gastric	stomach
2	chr5:40756400-40785200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:40756400-40797400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:40765400-40796600	Weak transcription	Right Ventricle	heart
5	chr5:40765600-40796600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:40766000-40782200	Weak transcription	Brain Substantia Nigra	brain
7	chr5:40771600-40788600	Weak transcription	Fetal Stomach	stomach
8	chr5:40773000-40788200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:40774800-40782200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:40776200-40782000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr5:40776200-40797000	Weak transcription	Colonic Mucosa	Colon
12	chr5:40776400-40781800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:40776400-40782000	Weak transcription	Colon Smooth Muscle	Colon
14	chr5:40776400-40784800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:40776600-40782000	Weak transcription	Small Intestine	intestine
16	chr5:40776600-40786200	Weak transcription	GM12878-XiMat	blood
17	chr5:40776600-40787600	Weak transcription	Hela-S3	cervix
18	chr5:40776800-40782000	Weak transcription	Brain Germinal Matrix	brain
19	chr5:40776800-40782800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr5:40776800-40784600	Weak transcription	HUVEC	blood vessel
21	chr5:40777000-40781600	Weak transcription	HSMM	muscle
22	chr5:40777000-40781800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:40777000-40781800	Weak transcription	NHLF	lung
24	chr5:40777000-40782000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:40777000-40782000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:40777000-40782000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:40777000-40782000	Weak transcription	Brain Hippocampus Middle	brain
28	chr5:40777000-40782000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr5:40777000-40782000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr5:40777000-40782000	Weak transcription	Fetal Lung	lung
31	chr5:40777000-40782000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr5:40777000-40782200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr5:40777000-40784000	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr5:40777000-40784200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr5:40777000-40784400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr5:40777000-40784400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr5:40777000-40784400	Weak transcription	Fetal Kidney	kidney
38	chr5:40777000-40787800	Weak transcription	HMEC	breast
39	chr5:40777000-40788000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr5:40777000-40788200	Weak transcription	Brain Anterior Caudate	brain
41	chr5:40777000-40789400	Weak transcription	Fetal Heart	heart
42	chr5:40777000-40796600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr5:40777000-40796600	Weak transcription	Thymus	Thymus
44	chr5:40777000-40796800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr5:40777000-40797000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr5:40777200-40781800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr5:40777200-40781800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:40777200-40781800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr5:40777200-40781800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr5:40777200-40782200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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