Variant report

Variant	rs12441483
Chromosome Location	chr15:40353416-40353417
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr15:40353284-40354130	GM12878	blood:	n/a	n/a
2	RUNX3	chr15:40353390-40354521	GM12878	blood:	n/a	n/a
3	MTA3	chr15:40353280-40354275	GM12878	blood:	n/a	n/a
4	CEBPB	chr15:40353309-40354162	GM12878	blood:	n/a	n/a
5	STAT5A	chr15:40353244-40354122	GM12878	blood:	n/a	n/a
6	NFYB	chr15:40353340-40353540	GM12878	blood:	n/a	n/a
7	RUNX3	chr15:40353380-40354200	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40351871..40354689-chr15:40374505..40376041,2	K562	blood:
2	chr15:40352649..40354633-chr15:40358305..40361225,2	K562	blood:
3	chr15:40350466..40352477-chr15:40353153..40356127,2	MCF-7	breast:
4	chr15:40351858..40353896-chr15:40357705..40360243,2	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EIF2AK4-2	chr15:40351566-40356802	XLOC_011219
2	lnc-EIF2AK4-2	chr15:40352298-40354374	NONHSAT041793
3	lnc-EIF2AK4-2	chr15:40352298-40354418	NONHSAT041803

No data

Variant related genes	Relation type
SRP14-AS1	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12440899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16970286	0.89[JPT][hapmap]
rs16970291	0.89[JPT][hapmap]
rs3803361	1.00[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4923848	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4923850	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4923851	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4924412	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]
rs4924414	0.88[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7162269	0.89[CEU][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7181230	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs7181985	0.94[ASW][hapmap];0.84[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7183386	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs749749	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9972424	0.89[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12441483	EIF2AK4	Cis_1M	lymphoblastoid	RTeQTL
rs12441483	EIF2AK4	cis	parietal	SCAN
rs12441483	RPUSD2	cis	parietal	SCAN
rs12441483	C15orf62	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

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	chr15:40343600-40355400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:40345600-40358800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:40346000-40367400	Weak transcription	K562	blood
6	chr15:40346200-40372800	Weak transcription	Fetal Kidney	kidney
7	chr15:40347400-40355400	Weak transcription	NH-A	brain
8	chr15:40347600-40361000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr15:40348000-40355000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:40348000-40355200	Weak transcription	Brain Anterior Caudate	brain
11	chr15:40348000-40355400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:40348000-40361000	Weak transcription	Fetal Intestine Large	intestine
13	chr15:40348200-40357200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr15:40348400-40355000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:40348400-40355000	Weak transcription	Right Ventricle	heart
16	chr15:40348400-40355200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:40348400-40355400	Weak transcription	Brain Germinal Matrix	brain
18	chr15:40348400-40355600	Weak transcription	Brain Hippocampus Middle	brain
19	chr15:40348400-40357000	Weak transcription	Spleen	Spleen
20	chr15:40348400-40358400	Enhancers	Fetal Thymus	thymus
21	chr15:40348400-40361000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr15:40348600-40354800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr15:40348600-40355400	Weak transcription	Left Ventricle	heart
24	chr15:40348600-40355600	Weak transcription	Colonic Mucosa	Colon
25	chr15:40348600-40361000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr15:40348600-40365800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:40348800-40354600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:40348800-40355000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr15:40348800-40355600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:40348800-40356400	Weak transcription	Primary B cells from cord blood	blood
31	chr15:40348800-40360600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr15:40348800-40365400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr15:40349000-40354600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:40349000-40354600	Weak transcription	HSMMtube	muscle
35	chr15:40349000-40355600	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:40349000-40355800	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr15:40349000-40357400	Weak transcription	Pancreas	Pancrea
38	chr15:40349000-40358600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:40349000-40360600	Weak transcription	Fetal Heart	heart
40	chr15:40349800-40355600	Weak transcription	Fetal Muscle Leg	muscle
41	chr15:40350600-40353600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:40351000-40354800	Weak transcription	NHDF-Ad	bronchial
43	chr15:40351000-40355000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:40351000-40356000	Weak transcription	Primary T cells from cord blood	blood
45	chr15:40351000-40356400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr15:40351000-40356400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr15:40351200-40354600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:40351200-40355000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:40351200-40355200	Weak transcription	NHLF	lung
50	chr15:40351400-40354800	Weak transcription	HMEC	breast

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