Variant report

Variant	rs12509236
Chromosome Location	chr4:119655888-119655889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr4:119655717-119656496	SK-N-SH	brain:	n/a	n/a
2	JUND	chr4:119655822-119656424	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr4:119655545-119656624	SK-N-SH	brain:	n/a	chr4:119656187-119656194
4	POLR2A	chr4:119655773-119656955	K562	blood:	n/a	n/a
5	PBX3	chr4:119655798-119656407	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr4:119655735-119656596	SK-N-SH	brain:	n/a	n/a
7	NFIC	chr4:119655721-119656354	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr4:119655694-119656558	SK-N-SH	brain:	n/a	chr4:119656187-119656194
9	TCF12	chr4:119655812-119656469	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119198265..119200504-chr4:119654029..119656125,2	K562	blood:

Variant related genes	Relation type
SEC24D	TF binding region
ENSG00000269893	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10014208	0.81[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap]
rs10470914	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs10518322	0.87[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes]
rs10518323	0.87[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes]
rs10518324	0.87[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes]
rs11098449	0.83[AMR][1000 genomes]
rs11098450	0.87[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes]
rs11722833	0.95[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11730993	0.88[AMR][1000 genomes]
rs11736024	0.86[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap];0.81[ASN][1000 genomes]
rs12500272	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12505513	0.83[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12509654	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12649666	0.81[ASN][1000 genomes]
rs13109947	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13109966	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13114964	0.87[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13120798	0.87[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13128195	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs13130107	0.91[EUR][1000 genomes]
rs17050423	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs298976	0.91[EUR][1000 genomes]
rs298977	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs298980	0.91[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs298981	0.91[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs298989	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs298990	0.91[CEU][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs298993	0.92[EUR][1000 genomes]
rs298997	0.91[EUR][1000 genomes]
rs299002	0.90[EUR][1000 genomes]
rs299003	0.90[EUR][1000 genomes]
rs299004	0.90[EUR][1000 genomes]
rs34371874	0.91[EUR][1000 genomes]
rs34384498	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34616305	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34730066	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35868882	0.85[AMR][1000 genomes]
rs3775836	0.90[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs399086	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs401950	0.90[EUR][1000 genomes]
rs428409	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs437027	0.91[EUR][1000 genomes]
rs439159	0.90[EUR][1000 genomes]
rs4834698	0.91[EUR][1000 genomes]
rs4834699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7676832	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs960738	0.86[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs960739	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv427693	chr4:119493919-119674742	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12509236	USP53	cis	cerebellum	SCAN
rs12509236	METTL14	cis	cerebellum	SCAN
rs12509236	AK026485	cis	multi-tissue	Pritchard
rs12509236	Contig37858_RC	cis	multi-tissue	Pritchard
rs12509236	METTL14	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119607200-119659200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:119607800-119693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:119608600-119674000	Weak transcription	Stomach Mucosa	stomach
4	chr4:119620000-119660200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:119625800-119718000	Weak transcription	Hela-S3	cervix
6	chr4:119628000-119659800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:119628400-119657600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr4:119630400-119674200	Weak transcription	A549	lung
9	chr4:119633200-119662800	Weak transcription	Brain Anterior Caudate	brain
10	chr4:119633400-119667600	Weak transcription	Brain Germinal Matrix	brain
11	chr4:119634400-119660000	Weak transcription	Brain Angular Gyrus	brain
12	chr4:119640600-119662200	Strong transcription	Fetal Muscle Trunk	muscle
13	chr4:119640800-119692600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr4:119641200-119659600	Strong transcription	Fetal Intestine Large	intestine
15	chr4:119641600-119659400	Strong transcription	Liver	Liver
16	chr4:119641600-119679800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr4:119642000-119661200	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:119642000-119662000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:119642000-119662000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr4:119642000-119666800	Strong transcription	Placenta	Placenta
21	chr4:119642200-119668200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr4:119642400-119656400	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr4:119642400-119662000	Strong transcription	Adipose Nuclei	Adipose
24	chr4:119642400-119662000	Strong transcription	Fetal Lung	lung
25	chr4:119642400-119668400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:119643000-119658400	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr4:119643000-119662000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:119644200-119659600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr4:119644400-119662000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr4:119644400-119662000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr4:119644400-119667400	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr4:119645400-119668200	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:119646200-119657800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr4:119646200-119662200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:119646200-119667000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:119646600-119662000	Strong transcription	GM12878-XiMat	blood
37	chr4:119647400-119660400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:119648800-119656400	Weak transcription	Colonic Mucosa	Colon
39	chr4:119649200-119659200	Weak transcription	Right Ventricle	heart
40	chr4:119649200-119665200	Weak transcription	Small Intestine	intestine
41	chr4:119649200-119666800	Weak transcription	Psoas Muscle	Psoas
42	chr4:119649200-119670600	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:119649200-119675200	Weak transcription	Brain Substantia Nigra	brain
44	chr4:119649200-119687600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:119649200-119693600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr4:119649400-119659400	Weak transcription	Fetal Kidney	kidney
47	chr4:119649600-119664600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr4:119649800-119656200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr4:119650600-119668400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:119651000-119659200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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