Variant report

Variant	rs4924412
Chromosome Location	chr15:40344885-40344886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40336937..40340971-chr15:40343981..40345656,3	K562	blood:
2	chr15:40330199..40332108-chr15:40344066..40345729,2	K562	blood:
3	chr15:40222962..40225062-chr15:40343455..40345112,2	K562	blood:
4	chr15:40343463..40345114-chr15:40397250..40398953,2	MCF-7	breast:
5	chr15:40343206..40345433-chr15:40385160..40387449,2	K562	blood:
6	chr15:40342956..40345791-chr15:40389827..40392011,2	MCF-7	breast:
7	chr15:40343530..40346228-chr15:40453102..40456209,3	K562	blood:
8	chr15:40343717..40348357-chr15:40394391..40397717,7	MCF-7	breast:
9	chr15:40343498..40345007-chr15:40348613..40351554,2	K562	blood:
10	chr15:40337344..40339688-chr15:40344036..40346311,2	K562	blood:
11	chr15:40344284..40346662-chr15:40350887..40352535,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000140319	Chromatin interaction
ENSG00000104081	Chromatin interaction
ENSG00000248508	Chromatin interaction
ENSG00000156970	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11638521	0.81[ASN][1000 genomes]
rs12440899	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441483	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16970286	0.89[JPT][hapmap]
rs16970291	0.89[JPT][hapmap]
rs16970319	0.80[JPT][hapmap]
rs3803361	0.85[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4923848	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923850	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4923851	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924414	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7162269	0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7181230	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs7181985	0.83[CEU][hapmap];0.84[CHB][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7183386	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749749	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972424	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv3326647	chr15:40340860-40345058	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4924412	EIF2AK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40337800-40355600	Weak transcription	Brain Angular Gyrus	brain
2	chr15:40337800-40355600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr15:40338000-40345200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:40338000-40347000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:40338200-40345000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:40339800-40347200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr15:40339800-40347600	Weak transcription	Brain Hippocampus Middle	brain
8	chr15:40340000-40346000	Weak transcription	Brain Germinal Matrix	brain
9	chr15:40340000-40346800	Weak transcription	Liver	Liver
10	chr15:40340400-40346000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:40340400-40347200	Weak transcription	Stomach Mucosa	stomach
12	chr15:40340600-40345200	Weak transcription	A549	lung
13	chr15:40340600-40345800	Weak transcription	NHDF-Ad	bronchial
14	chr15:40340600-40347600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:40340800-40345000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr15:40340800-40345400	Enhancers	Dnd41	blood
17	chr15:40340800-40345400	Weak transcription	Osteobl	bone
18	chr15:40340800-40346000	Weak transcription	NHLF	lung
19	chr15:40340800-40346200	Weak transcription	NH-A	brain
20	chr15:40340800-40346400	Weak transcription	HMEC	breast
21	chr15:40340800-40347000	Weak transcription	Brain Substantia Nigra	brain
22	chr15:40340800-40347000	Weak transcription	Esophagus	oesophagus
23	chr15:40340800-40349600	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr15:40341000-40346400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr15:40341000-40346400	Enhancers	Primary T cells from cord blood	blood
26	chr15:40341000-40347200	Weak transcription	Brain Anterior Caudate	brain
27	chr15:40341000-40347200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr15:40341200-40345800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr15:40341600-40345000	Weak transcription	HSMMtube	muscle
30	chr15:40341800-40346200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:40342600-40345200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr15:40342600-40345800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:40342600-40346200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:40342600-40346200	Weak transcription	Psoas Muscle	Psoas
35	chr15:40342600-40346400	Weak transcription	Adipose Nuclei	Adipose
36	chr15:40342800-40345200	Weak transcription	Primary B cells from cord blood	blood
37	chr15:40342800-40345600	Enhancers	Fetal Thymus	thymus
38	chr15:40342800-40348600	Enhancers	Colonic Mucosa	Colon
39	chr15:40343000-40345000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:40343000-40345000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:40343000-40345000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:40343000-40345200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr15:40343000-40345400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr15:40343000-40345600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr15:40343000-40345800	Enhancers	Fetal Intestine Small	intestine
46	chr15:40343000-40345800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr15:40343000-40346000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr15:40343000-40346200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr15:40343000-40346200	Weak transcription	Left Ventricle	heart
50	chr15:40343000-40346400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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