Variant report

Variant	rs12439335
Chromosome Location	chr15:40245114-40245115
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10518676	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10851392	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11632930	0.87[CEU][hapmap]
rs11633416	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12324733	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12438989	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12439021	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12441927	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12442713	0.88[CEU][hapmap]
rs12906976	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1656894	1.00[ASN][1000 genomes]
rs1656895	0.87[ASN][1000 genomes]
rs2247984	0.87[ASN][1000 genomes]
rs2412451	0.88[ASN][1000 genomes]
rs2934194	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs34298786	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs480095	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs486816	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs489424	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs494614	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs494690	0.87[ASN][1000 genomes]
rs518770	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs527610	0.89[ASN][1000 genomes]
rs534757	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs535407	0.85[ASN][1000 genomes]
rs552251	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs55957853	0.81[ASN][1000 genomes]
rs56143280	0.81[ASN][1000 genomes]
rs562159	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs577289	0.81[CHB][hapmap];0.81[YRI][hapmap];0.85[ASN][1000 genomes]
rs580836	0.93[JPT][hapmap]
rs581233	0.84[ASN][1000 genomes]
rs8030025	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8030640	0.91[CEU][hapmap];0.85[JPT][hapmap]
rs8030687	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs8035930	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8042788	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9302104	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv832983	chr15:40098766-40248839	Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12439335	EIF2AK4	cis	lesional skin	skin_eQTL
rs12439335	EIF2AK4	Cis_1M	lymphoblastoid	RTeQTL
rs12439335	EIF2AK4	cis	normal skin	skin_eQTL
rs12439335	EIF2AK4	cis	uninvolved skin	skin_eQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40227200-40247800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:40227200-40248200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr15:40227200-40268400	Weak transcription	Esophagus	oesophagus
4	chr15:40227400-40283400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:40227800-40247000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:40227800-40268400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:40228200-40323800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:40228600-40246000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr15:40230000-40263000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr15:40230200-40255600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:40230400-40261600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:40230600-40252400	Weak transcription	Right Atrium	heart
13	chr15:40231000-40268400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:40231800-40252600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:40232000-40261400	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:40232000-40262600	Strong transcription	Liver	Liver
17	chr15:40232200-40250200	Strong transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:40232200-40252400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr15:40232400-40252400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr15:40232600-40251000	Strong transcription	Left Ventricle	heart
21	chr15:40232600-40251800	Strong transcription	Adipose Nuclei	Adipose
22	chr15:40233400-40248600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr15:40235000-40245400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:40235000-40263000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr15:40236000-40255400	Strong transcription	Fetal Lung	lung
26	chr15:40236000-40260000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr15:40236600-40245600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr15:40236600-40303000	Weak transcription	Small Intestine	intestine
29	chr15:40237800-40255600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr15:40238000-40277800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:40238200-40245800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr15:40238200-40247000	Weak transcription	K562	blood
33	chr15:40238600-40268200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr15:40238600-40272200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:40238800-40245600	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:40238800-40247000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr15:40238800-40248600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:40238800-40273200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr15:40239000-40247200	Weak transcription	Fetal Heart	heart
40	chr15:40239200-40245600	Strong transcription	HMEC	breast
41	chr15:40239200-40259600	Weak transcription	Fetal Brain Male	brain
42	chr15:40239400-40245600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:40239400-40245600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr15:40239400-40261200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:40239400-40262000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:40239600-40251400	Strong transcription	Osteobl	bone
47	chr15:40239600-40261400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:40239800-40262200	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr15:40240000-40251200	Strong transcription	NHDF-Ad	bronchial
50	chr15:40240200-40261000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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