Variant report

Variant	rs518770
Chromosome Location	chr15:40230272-40230273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40229592..40232306-chr15:40232969..40235787,3	K562	blood:
2	chr15:40227974..40230444-chr15:40236467..40239295,4	K562	blood:
3	chr15:40225691..40227971-chr15:40229270..40234553,6	MCF-7	breast:
4	chr15:40086220..40089106-chr15:40229459..40231210,2	K562	blood:
5	chr15:40226141..40228971-chr15:40229388..40231436,2	K562	blood:
6	chr15:40213996..40216458-chr15:40228860..40231752,2	K562	blood:
7	chr15:40229592..40232306-chr15:40232969..40236218,4	K562	blood:

Variant related genes	Relation type
ENSG00000200305	Chromatin interaction
ENSG00000128829	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10518676	0.84[JPT][hapmap]
rs10851392	0.82[JPT][hapmap]
rs11633416	0.84[JPT][hapmap]
rs12324733	0.82[JPT][hapmap]
rs12439335	0.81[CHB][hapmap];0.87[ASN][1000 genomes]
rs1656894	0.87[ASN][1000 genomes]
rs1656895	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1656896	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2247984	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412451	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2917497	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2934194	0.82[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs480095	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486816	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489424	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494614	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494690	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500200	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs508281	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs524240	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs525910	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs527610	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs534757	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535407	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs552251	0.82[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs562159	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577289	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs580836	0.91[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs581233	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8030025	0.84[JPT][hapmap]
rs8030687	0.83[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs518770	EIF2AK4	cis	Artery Tibial	GTEx
rs518770	FAM98B	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40227200-40232000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr15:40227200-40232200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr15:40227200-40232200	Weak transcription	Colonic Mucosa	Colon
4	chr15:40227200-40232200	Weak transcription	Placenta	Placenta
5	chr15:40227200-40232200	Weak transcription	Left Ventricle	heart
6	chr15:40227200-40235800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:40227200-40236000	Weak transcription	Brain Angular Gyrus	brain
8	chr15:40227200-40247800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:40227200-40248200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:40227200-40268400	Weak transcription	Esophagus	oesophagus
11	chr15:40227400-40230400	Enhancers	Liver	Liver
12	chr15:40227400-40230800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:40227400-40230800	Weak transcription	Fetal Stomach	stomach
14	chr15:40227400-40230800	Weak transcription	Psoas Muscle	Psoas
15	chr15:40227400-40231000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr15:40227400-40231800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr15:40227400-40232000	Weak transcription	Brain Substantia Nigra	brain
18	chr15:40227400-40232000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:40227400-40232200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:40227400-40232200	Weak transcription	Brain Hippocampus Middle	brain
21	chr15:40227400-40232200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:40227400-40233000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr15:40227400-40234000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:40227400-40235000	Weak transcription	Fetal Brain Female	brain
25	chr15:40227400-40236000	Weak transcription	Brain Germinal Matrix	brain
26	chr15:40227400-40236800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr15:40227400-40237600	Weak transcription	Fetal Brain Male	brain
28	chr15:40227400-40283400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr15:40227600-40231800	Weak transcription	Fetal Kidney	kidney
30	chr15:40227600-40235800	Weak transcription	Small Intestine	intestine
31	chr15:40227800-40230400	Weak transcription	Ovary	ovary
32	chr15:40227800-40230400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:40227800-40230800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:40227800-40232000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:40227800-40232200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:40227800-40232200	Weak transcription	Fetal Lung	lung
37	chr15:40227800-40232200	Weak transcription	Lung	lung
38	chr15:40227800-40233200	Weak transcription	K562	blood
39	chr15:40227800-40235000	Weak transcription	Right Ventricle	heart
40	chr15:40227800-40237600	Weak transcription	Gastric	stomach
41	chr15:40227800-40247000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr15:40227800-40268400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr15:40228000-40230800	Weak transcription	Primary B cells from cord blood	blood
44	chr15:40228000-40230800	Weak transcription	Fetal Thymus	thymus
45	chr15:40228000-40231000	Weak transcription	Brain Anterior Caudate	brain
46	chr15:40228000-40231000	Weak transcription	Fetal Heart	heart
47	chr15:40228000-40231800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr15:40228000-40232200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr15:40228000-40233000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr15:40228000-40233400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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