Variant report

Variant	rs1013758
Chromosome Location	chr3:43626375-43626376
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:43624986..43626913-chr3:43630148..43631956,2	K562	blood:
2	chr3:43624986..43627370-chr3:43630211..43632128,5	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1038202	0.81[EUR][1000 genomes]
rs10461013	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10461015	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11130004	0.92[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs11130005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12374079	0.83[EUR][1000 genomes]
rs12486736	0.94[EUR][1000 genomes]
rs12492694	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12638282	0.92[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs13066902	0.81[ASN][1000 genomes]
rs13319147	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13433789	0.81[AMR][1000 genomes]
rs1351631	0.92[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs1384435	0.92[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs1564434	0.92[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs17408925	0.81[EUR][1000 genomes]
rs1842806	0.87[EUR][1000 genomes]
rs1842807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1975997	0.92[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs2054553	0.83[EUR][1000 genomes]
rs2054554	0.83[EUR][1000 genomes]
rs2101064	0.88[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs2127725	0.81[EUR][1000 genomes]
rs3772160	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772165	0.83[EUR][1000 genomes]
rs3821381	0.83[EUR][1000 genomes]
rs3902207	0.82[EUR][1000 genomes]
rs4128530	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4264704	0.90[EUR][1000 genomes]
rs4407383	0.89[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap]
rs4505672	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs4547674	0.88[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap]
rs4682690	0.83[EUR][1000 genomes]
rs61102363	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6441786	0.82[EUR][1000 genomes]
rs6763321	0.82[EUR][1000 genomes]
rs6769576	0.85[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap]
rs737516	0.92[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.94[EUR][1000 genomes]
rs7616708	0.83[EUR][1000 genomes]
rs7621271	0.83[EUR][1000 genomes]
rs9311340	0.92[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs9311341	0.83[EUR][1000 genomes]
rs9809643	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9814737	0.93[EUR][1000 genomes]
rs9815196	0.92[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs9824990	0.88[CEU][hapmap]
rs9826275	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9829067	0.94[EUR][1000 genomes]
rs9830697	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs9834786	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9835793	0.90[EUR][1000 genomes]
rs9851894	0.81[EUR][1000 genomes]
rs9852783	0.81[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862259	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs9873316	0.93[EUR][1000 genomes]
rs9878330	0.83[EUR][1000 genomes]
rs9881028	0.85[EUR][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	nsv428738	chr3:43491435-43651168	Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv834673	chr3:43622985-43799876	Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1013758	SNRK	cis	cerebellum	SCAN
rs1013758	PTH1R	cis	parietal	SCAN
rs1013758	MRPS18A	trans	cerebellum	SCAN
rs1013758	RPL14	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43574800-43662400	Weak transcription	Right Ventricle	heart
2	chr3:43580600-43647600	Weak transcription	Brain Angular Gyrus	brain
3	chr3:43584000-43632800	Weak transcription	Small Intestine	intestine
4	chr3:43587000-43647200	Weak transcription	Fetal Kidney	kidney
5	chr3:43587200-43632000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr3:43587800-43634000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:43589000-43648400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:43590600-43636400	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr3:43595000-43632600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:43595800-43632800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:43596600-43632000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:43596600-43632600	Weak transcription	HSMMtube	muscle
13	chr3:43597200-43628800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:43601600-43631800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:43602000-43632600	Weak transcription	Esophagus	oesophagus
16	chr3:43602600-43632800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:43607600-43627000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr3:43614000-43632600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:43614000-43632600	Weak transcription	Fetal Intestine Small	intestine
20	chr3:43614400-43632400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:43614400-43632600	Weak transcription	Gastric	stomach
22	chr3:43614600-43653800	Weak transcription	HepG2	liver
23	chr3:43616800-43633200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr3:43618400-43639400	Weak transcription	Liver	Liver
25	chr3:43618600-43627000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:43618600-43632600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:43618600-43632600	Weak transcription	Adipose Nuclei	Adipose
28	chr3:43618600-43632600	Weak transcription	Fetal Intestine Large	intestine
29	chr3:43618600-43632600	Weak transcription	Placenta	Placenta
30	chr3:43618600-43633000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:43618600-43644000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr3:43618600-43649600	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:43618600-43654400	Weak transcription	Colonic Mucosa	Colon
34	chr3:43618600-43662400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:43618800-43626600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:43618800-43627000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:43618800-43627000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:43618800-43632600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:43618800-43632800	Weak transcription	Left Ventricle	heart
40	chr3:43619000-43631400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:43619600-43631800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:43619600-43632600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:43619600-43632800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:43619800-43632600	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr3:43620000-43632600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:43621800-43632200	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:43622000-43627600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:43622000-43627600	Weak transcription	Ovary	ovary
49	chr3:43622000-43632400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr3:43622000-43632600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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