Variant report

Variant	rs2934194
Chromosome Location	chr15:40239912-40239913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40238602..40241271-chr15:40241426..40244284,2	K562	blood:
2	chr15:40232628..40236557-chr15:40238241..40241740,4	K562	blood:

Variant related genes	Relation type
ENSG00000259389	Chromatin interaction
ENSG00000238564	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10518676	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10851392	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11631801	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11632930	0.95[CEU][hapmap];0.95[GIH][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11633416	0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.86[ASN][1000 genomes]
rs12324733	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12438989	0.84[ASN][1000 genomes]
rs12439021	0.84[ASN][1000 genomes]
rs12439335	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs12441927	0.84[ASN][1000 genomes]
rs12442713	0.80[CEU][hapmap];0.87[GIH][hapmap]
rs12906976	0.84[ASN][1000 genomes]
rs1656894	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1656895	0.89[ASN][1000 genomes]
rs16970134	0.82[EUR][1000 genomes]
rs2247984	0.89[ASN][1000 genomes]
rs2412451	0.91[ASN][1000 genomes]
rs28617639	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2917497	0.81[ASN][1000 genomes]
rs480095	0.82[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs486816	0.82[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs489424	0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs494614	0.82[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs494690	0.89[ASN][1000 genomes]
rs508281	0.81[ASN][1000 genomes]
rs518770	0.82[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs527610	0.92[ASN][1000 genomes]
rs534757	0.82[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs535407	0.87[ASN][1000 genomes]
rs552251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55957853	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56143280	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs562159	0.82[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs577289	0.82[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs580836	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs581233	0.87[ASN][1000 genomes]
rs72729488	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8030025	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap];0.86[ASN][1000 genomes]
rs8030640	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8030687	1.00[CEU][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8030980	0.87[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8035930	0.84[ASN][1000 genomes]
rs8042788	0.86[ASN][1000 genomes]
rs9302104	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2934194	EIF2AK4	cis	lesional skin	skin_eQTL
rs2934194	EIF2AK4	cis	cerebellum	SCAN
rs2934194	EIF2AK4	Cis_1M	lymphoblastoid	RTeQTL
rs2934194	RAD51	cis	parietal	SCAN
rs2934194	NOP10	cis	cerebellum	SCAN

Chromatin state (count:126 , 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	chr15:40230400-40240000	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr15:40230400-40261600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:40230600-40252400	Weak transcription	Right Atrium	heart
14	chr15:40230800-40240000	Strong transcription	Fetal Stomach	stomach
15	chr15:40231000-40268400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:40231400-40243400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr15:40231800-40240200	Strong transcription	Fetal Muscle Leg	muscle
18	chr15:40231800-40243400	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr15:40231800-40252600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr15:40232000-40240000	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr15:40232000-40240400	Strong transcription	Primary B cells from cord blood	blood
22	chr15:40232000-40261400	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr15:40232000-40262600	Strong transcription	Liver	Liver
24	chr15:40232200-40240000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:40232200-40240000	Strong transcription	Stomach Smooth Muscle	stomach
26	chr15:40232200-40240200	Strong transcription	Fetal Thymus	thymus
27	chr15:40232200-40241600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:40232200-40244600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr15:40232200-40250200	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:40232200-40252400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr15:40232400-40240000	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr15:40232400-40252400	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr15:40232600-40240000	Strong transcription	GM12878-XiMat	blood
34	chr15:40232600-40240400	Strong transcription	Duodenum Mucosa	Duodenum
35	chr15:40232600-40251000	Strong transcription	Left Ventricle	heart
36	chr15:40232600-40251800	Strong transcription	Adipose Nuclei	Adipose
37	chr15:40233400-40248600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr15:40234000-40240000	Strong transcription	HUVEC	blood vessel
39	chr15:40234800-40240000	Strong transcription	Brain Substantia Nigra	brain
40	chr15:40234800-40240000	Strong transcription	Placenta	Placenta
41	chr15:40234800-40244200	Strong transcription	NHEK	skin
42	chr15:40235000-40241800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr15:40235000-40242200	Strong transcription	Fetal Brain Female	brain
44	chr15:40235000-40245000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:40235000-40245400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:40235000-40263000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:40235200-40241800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:40235200-40241800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:40235200-40243400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr15:40235200-40244200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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