Variant report

Variant	rs829112
Chromosome Location	chr12:51207704-51207705
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	chr12:51206635..51209642-chr12:51213405..51216758,3	K562	blood:
2	chr12:51207076..51210339-chr12:51211809..51214905,4	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10735827	0.91[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs10747586	1.00[ASN][1000 genomes]
rs10747592	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs10783377	1.00[ASN][1000 genomes]
rs10783380	1.00[ASN][1000 genomes]
rs10783388	0.91[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs1109726	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609941	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345538	1.00[CHB][hapmap]
rs1521516	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs1561422	0.95[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs2250751	1.00[ASN][1000 genomes]
rs2250752	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2251024	1.00[ASN][1000 genomes]
rs2251603	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs2252589	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2554862	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2684889	1.00[ASN][1000 genomes]
rs2684898	1.00[ASN][1000 genomes]
rs2684900	1.00[ASN][1000 genomes]
rs2684901	1.00[ASN][1000 genomes]
rs2700479	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2700480	1.00[ASN][1000 genomes]
rs2700482	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs2700485	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2731434	1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2731439	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2731440	1.00[ASN][1000 genomes]
rs2731442	1.00[ASN][1000 genomes]
rs2731443	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4768862	0.85[EUR][1000 genomes]
rs57602501	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57729468	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580769	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66838741	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66947035	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67218241	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67356137	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67934435	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135837	1.00[ASN][1000 genomes]
rs7305655	1.00[ASN][1000 genomes]
rs7307788	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7487150	0.84[EUR][1000 genomes]
rs7958114	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7960015	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964642	0.86[EUR][1000 genomes]
rs7968440	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7976942	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977064	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977690	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7977742	1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes]
rs7978559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979165	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829114	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829115	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs861204	1.00[CHB][hapmap];0.85[MEX][hapmap]
rs864899	0.90[YRI][hapmap]
rs865489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv976745	chr12:51203441-51215185	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs829112	LASS5	cis	multi-tissue	Pritchard
rs829112	KIAA1463	cis	multi-tissue	Pritchard
rs829112	LASS5	cis	parietal	SCAN
rs829112	DIP2B	cis	cerebellum	SCAN
rs829112	DHH	cis	parietal	SCAN
rs829112	AMIGO2	cis	cerebellum	SCAN
rs829112	CERS5	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51188600-51207800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:51190200-51215200	Weak transcription	Pancreas	Pancrea
3	chr12:51193200-51207800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:51193200-51207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:51193200-51207800	Weak transcription	Esophagus	oesophagus
6	chr12:51193200-51208000	Weak transcription	Small Intestine	intestine
7	chr12:51193200-51211200	Weak transcription	Aorta	Aorta
8	chr12:51193400-51207800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:51194400-51207800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:51194600-51207800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:51194600-51214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:51194800-51209200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:51198600-51215400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr12:51199600-51209400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:51200400-51209200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:51200600-51222200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:51201400-51213800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:51201600-51212400	Strong transcription	Fetal Lung	lung
19	chr12:51201600-51213200	Strong transcription	Fetal Muscle Leg	muscle
20	chr12:51201800-51212200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:51201800-51212200	Strong transcription	Fetal Intestine Large	intestine
22	chr12:51201800-51212400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:51201800-51213800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:51202000-51213000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:51202000-51213200	Strong transcription	Fetal Stomach	stomach
26	chr12:51202200-51213200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:51202200-51213200	Strong transcription	Fetal Intestine Small	intestine
28	chr12:51202200-51213800	Strong transcription	Fetal Thymus	thymus
29	chr12:51202200-51214200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:51202600-51213800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:51202600-51214400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr12:51202800-51208600	Strong transcription	Hela-S3	cervix
33	chr12:51202800-51213600	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr12:51202800-51214000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:51202800-51215000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:51203200-51212400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr12:51203200-51213400	Strong transcription	Primary B cells from cord blood	blood
38	chr12:51203200-51213800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr12:51203200-51213800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:51203200-51213800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr12:51203200-51213800	Strong transcription	Adipose Nuclei	Adipose
42	chr12:51203200-51213800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr12:51203200-51214000	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr12:51203200-51214000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr12:51203200-51214200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:51203200-51214200	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr12:51203400-51208600	Strong transcription	K562	blood
48	chr12:51203400-51211000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:51203400-51213200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:51203400-51213600	Strong transcription	Primary B cells from peripheral blood	blood

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