Variant report

Variant	rs60994254
Chromosome Location	chr3:42677354-42677355
allele	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:40)

rs_ID	r²[population]
rs13064311	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13066173	0.82[ASN][1000 genomes]
rs13066333	0.82[ASN][1000 genomes]
rs168138	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2068278	0.82[ASN][1000 genomes]
rs2271181	0.82[ASN][1000 genomes]
rs2271184	0.84[ASN][1000 genomes]
rs2271187	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2284305	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs237064	0.82[ASN][1000 genomes]
rs2940407	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3095258	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs339656	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs339720	0.92[ASN][1000 genomes]
rs339721	0.94[ASN][1000 genomes]
rs339724	0.90[ASN][1000 genomes]
rs339729	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs339735	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342534	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs342535	0.81[ASN][1000 genomes]
rs342538	0.82[ASN][1000 genomes]
rs383937	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3888651	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs398743	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs612362	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs637852	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs638904	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs651180	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs654761	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs663258	0.82[ASN][1000 genomes]
rs664813	0.87[ASN][1000 genomes]
rs665206	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs704982	0.86[ASN][1000 genomes]
rs807863	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs82755	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9311323	0.88[ASN][1000 genomes]
rs9311324	0.90[ASN][1000 genomes]
rs9813479	0.94[ASN][1000 genomes]
rs9819563	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9828279	0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60994254	SEC22C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42647200-42688200	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr3:42647600-42677600	Weak transcription	Gastric	stomach
3	chr3:42651200-42693000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:42651800-42680400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:42655000-42677800	Weak transcription	Small Intestine	intestine
6	chr3:42656200-42688400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr3:42657400-42679600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:42658200-42682200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:42658200-42693000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:42658400-42691400	Strong transcription	Dnd41	blood
11	chr3:42658600-42677600	Weak transcription	Psoas Muscle	Psoas
12	chr3:42658600-42678400	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:42659000-42688000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:42660000-42679000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:42665000-42679400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr3:42668000-42688200	Strong transcription	Fetal Thymus	thymus
17	chr3:42668400-42692800	Strong transcription	Fetal Muscle Trunk	muscle
18	chr3:42668600-42678200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr3:42668800-42679800	Strong transcription	Osteobl	bone
20	chr3:42668800-42689200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:42668800-42690200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:42669000-42690600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:42669200-42691800	Strong transcription	Fetal Intestine Large	intestine
24	chr3:42669200-42692200	Strong transcription	Liver	Liver
25	chr3:42669400-42690600	Strong transcription	K562	blood
26	chr3:42669400-42691600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:42669400-42692200	Strong transcription	Fetal Muscle Leg	muscle
28	chr3:42669600-42690000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr3:42669600-42691000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:42669800-42679600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr3:42669800-42680600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:42670000-42677600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:42670200-42678400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:42671000-42690800	Strong transcription	Placenta	Placenta
35	chr3:42671200-42678800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:42671200-42679000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:42671200-42681400	Strong transcription	Fetal Brain Male	brain
38	chr3:42671200-42690800	Strong transcription	NHDF-Ad	bronchial
39	chr3:42671200-42691400	Strong transcription	HSMM	muscle
40	chr3:42671200-42691600	Strong transcription	NH-A	brain
41	chr3:42671400-42678200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:42671400-42680400	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:42671400-42680600	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:42671400-42682000	Strong transcription	NHEK	skin
45	chr3:42671400-42682200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:42671400-42682200	Strong transcription	HUVEC	blood vessel
47	chr3:42671400-42683000	Strong transcription	HSMMtube	muscle
48	chr3:42671400-42687600	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:42671400-42689800	Strong transcription	Primary B cells from cord blood	blood
50	chr3:42671400-42690600	Strong transcription	Fetal Lung	lung

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