Variant report

Variant	rs11749180
Chromosome Location	chr5:40745746-40745747
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40745635..40751387-chr5:40751429..40754891,8	K562	blood:
2	chr5:40743527..40746341-chr5:40834404..40836606,2	MCF-7	breast:
3	chr5:40745599..40747692-chr5:40753558..40755440,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145592	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10064650	1.00[ASW][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap]
rs1070444	0.88[GIH][hapmap];0.94[TSI][hapmap]
rs11740266	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]
rs11743132	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11743196	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11745121	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[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748743	0.91[EUR][1000 genomes]
rs11749437	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186450	0.83[AMR][1000 genomes]
rs12188129	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]
rs12188981	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35999176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357568	0.83[AMR][1000 genomes]
rs62357569	0.83[AMR][1000 genomes]
rs62357570	0.83[AMR][1000 genomes]
rs62357571	0.83[AMR][1000 genomes]
rs704034	0.88[GIH][hapmap];0.89[TSI][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11749180	GDNF	cis	cerebellum	SCAN
rs11749180	ZNF131	cis	cerebellum	SCAN
rs11749180	NVL	trans	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40722800-40755200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:40736000-40747200	Weak transcription	HMEC	breast
3	chr5:40736000-40755200	Weak transcription	Pancreas	Pancrea
4	chr5:40736200-40754200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr5:40736400-40746400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr5:40736400-40747000	Weak transcription	Small Intestine	intestine
7	chr5:40736400-40753800	Weak transcription	Fetal Heart	heart
8	chr5:40736400-40754200	Weak transcription	Gastric	stomach
9	chr5:40736400-40754200	Weak transcription	NHLF	lung
10	chr5:40736600-40754200	Weak transcription	Osteobl	bone
11	chr5:40738000-40754200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr5:40739400-40754200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:40739800-40754200	Weak transcription	NHEK	skin
14	chr5:40740200-40745800	Strong transcription	Hela-S3	cervix
15	chr5:40740800-40746400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr5:40740800-40754200	Weak transcription	HSMMtube	muscle
17	chr5:40741000-40754200	Weak transcription	Colonic Mucosa	Colon
18	chr5:40741200-40746000	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr5:40741600-40746600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:40741600-40754200	Weak transcription	K562	blood
21	chr5:40741800-40745800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr5:40741800-40746200	Weak transcription	HUVEC	blood vessel
23	chr5:40741800-40746400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:40741800-40746600	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:40741800-40746600	Weak transcription	A549	lung
26	chr5:40741800-40746800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:40741800-40746800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:40741800-40746800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr5:40741800-40751200	Weak transcription	Primary hematopoietic stem cells	blood
30	chr5:40741800-40752000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:40741800-40753800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr5:40741800-40754000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr5:40741800-40754200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr5:40741800-40754200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr5:40741800-40754200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr5:40741800-40754200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr5:40741800-40754200	Weak transcription	Fetal Brain Male	brain
38	chr5:40741800-40754200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr5:40741800-40754200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr5:40741800-40754200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr5:40741800-40754200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr5:40741800-40754200	Weak transcription	NH-A	brain
43	chr5:40741800-40754400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:40741800-40754400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:40741800-40754400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr5:40742000-40746200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:40742000-40746400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr5:40742000-40746800	Weak transcription	Stomach Mucosa	stomach
49	chr5:40742000-40747000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:40742000-40747000	Weak transcription	Right Ventricle	heart

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