Variant report

Variant	rs17538775
Chromosome Location	chr12:32732329-32732330
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1004969	1.00[ASW][hapmap]
rs10506094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10844245	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10844246	0.83[AMR][1000 genomes]
rs10844248	0.84[AMR][1000 genomes]
rs11052070	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11052071	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11052072	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11052073	0.94[AMR][1000 genomes]
rs11052076	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11052078	0.92[ASN][1000 genomes]
rs11052079	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11052081	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11052082	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11052083	0.83[AMR][1000 genomes]
rs11052084	0.94[ASN][1000 genomes]
rs11052085	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11052087	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11052088	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11052092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16920058	1.00[CHB][hapmap]
rs17539491	1.00[ASW][hapmap]
rs17539848	1.00[ASW][hapmap]
rs2102043	0.97[ASN][1000 genomes]
rs35861269	0.84[AMR][1000 genomes]
rs4525322	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4575368	1.00[ASW][hapmap]
rs4931019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4931028	0.89[EUR][1000 genomes]
rs61926167	0.87[ASN][1000 genomes]
rs6488066	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[ASN][1000 genomes]
rs73081434	0.85[AMR][1000 genomes]
rs73081435	0.84[AMR][1000 genomes]
rs73081444	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73081467	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73100149	0.82[AMR][1000 genomes]
rs7313539	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7961549	1.00[CHB][hapmap];0.97[ASN][1000 genomes]

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	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17538775	H3F3C	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32712600-32738600	Weak transcription	Primary B cells from cord blood	blood
2	chr12:32713000-32780400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:32713400-32796200	Weak transcription	Fetal Lung	lung
4	chr12:32713800-32738400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:32714000-32740600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr12:32715200-32735000	Weak transcription	Placenta	Placenta
7	chr12:32715200-32753800	Weak transcription	Fetal Brain Female	brain
8	chr12:32715200-32760200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:32719800-32741400	Weak transcription	Spleen	Spleen
10	chr12:32720000-32764800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:32720200-32778400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:32721400-32743600	Weak transcription	Fetal Heart	heart
13	chr12:32722200-32738600	Weak transcription	Brain Anterior Caudate	brain
14	chr12:32722400-32734800	Weak transcription	Brain Germinal Matrix	brain
15	chr12:32722600-32734800	Weak transcription	Small Intestine	intestine
16	chr12:32722600-32735000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr12:32722600-32735000	Weak transcription	NH-A	brain
18	chr12:32722600-32739200	Weak transcription	NHLF	lung
19	chr12:32722600-32740800	Weak transcription	Brain Angular Gyrus	brain
20	chr12:32722600-32754400	Weak transcription	Colonic Mucosa	Colon
21	chr12:32722600-32757600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:32722600-32764800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:32722600-32764800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:32722600-32764800	Weak transcription	Psoas Muscle	Psoas
25	chr12:32722600-32779400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr12:32723000-32735000	Weak transcription	Brain Substantia Nigra	brain
27	chr12:32723600-32756600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:32724200-32735000	Weak transcription	Lung	lung
29	chr12:32724600-32734800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr12:32724600-32735000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr12:32724600-32735000	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr12:32725000-32735000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:32725000-32739600	Weak transcription	Right Atrium	heart
34	chr12:32725200-32743800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:32725200-32778600	Weak transcription	Fetal Brain Male	brain
36	chr12:32726000-32741600	Weak transcription	Stomach Mucosa	stomach
37	chr12:32726400-32737200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:32727200-32736200	Weak transcription	Fetal Kidney	kidney
39	chr12:32727200-32736200	Weak transcription	NHDF-Ad	bronchial
40	chr12:32727400-32734800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:32727600-32737400	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr12:32727600-32738000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:32728000-32732600	Weak transcription	Brain Hippocampus Middle	brain
44	chr12:32728000-32738600	Strong transcription	Liver	Liver
45	chr12:32728200-32733600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:32728200-32735800	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:32728200-32737800	Strong transcription	HSMM	muscle
48	chr12:32728400-32738600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:32728600-32735000	Weak transcription	Aorta	Aorta
50	chr12:32728600-32757000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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