Variant report

Variant	rs4774924
Chromosome Location	chr15:57602999-57603000
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57602461..57607778-chr15:57612282..57619576,11	K562	blood:
2	chr15:57595866..57598853-chr15:57602406..57604089,3	K562	blood:
3	chr15:57601950..57604007-chr15:57607354..57609319,2	K562	blood:
4	chr15:57600919..57606103-chr15:57620754..57624822,5	K562	blood:
5	chr15:57599033..57602011-chr15:57602301..57604910,2	MCF-7	breast:
6	chr15:57598904..57601336-chr15:57602570..57606633,5	K562	blood:
7	chr15:57595866..57598518-chr15:57602406..57603938,2	K562	blood:

Variant related genes	Relation type
ENSG00000260870	Chromatin interaction
ENSG00000247982	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10152785	0.80[EUR][1000 genomes]
rs10459625	0.81[JPT][hapmap]
rs11071311	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11631073	0.85[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs11855537	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12904145	0.96[CEU][hapmap];0.84[CHB][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12905158	0.84[CEU][hapmap]
rs12913286	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17820184	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414501	0.88[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2431018	0.85[CEU][hapmap]
rs2440941	0.81[EUR][1000 genomes]
rs2544132	0.96[CEU][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs2591053	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2591054	0.87[CEU][hapmap]
rs4534776	0.85[JPT][hapmap]
rs4774256	0.90[JPT][hapmap]
rs4774923	0.85[CEU][hapmap];0.88[YRI][hapmap];0.88[EUR][1000 genomes]
rs4774925	0.82[CEU][hapmap]
rs4774926	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4774927	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4774928	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61999614	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7170975	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs8027325	0.84[AMR][1000 genomes];0.94[EUR][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	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1054547	chr15:57600488-57977659	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4774924	LINC00926	cis	Artery Tibial	GTEx
rs4774924	TEX9	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57599000-57603000	Weak transcription	K562	blood
2	chr15:57599400-57604600	Weak transcription	Right Ventricle	heart
3	chr15:57599400-57605000	Weak transcription	Fetal Brain Female	brain
4	chr15:57599400-57612800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr15:57599600-57603800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr15:57599600-57604600	Weak transcription	Fetal Thymus	thymus
7	chr15:57599600-57604600	Weak transcription	Left Ventricle	heart
8	chr15:57599600-57604600	Weak transcription	Pancreas	Pancrea
9	chr15:57599600-57604600	Weak transcription	Psoas Muscle	Psoas
10	chr15:57599600-57604600	Weak transcription	Right Atrium	heart
11	chr15:57599600-57604800	Weak transcription	Fetal Brain Male	brain
12	chr15:57599600-57612400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:57599600-57612800	Weak transcription	GM12878-XiMat	blood
14	chr15:57599600-57614200	Weak transcription	Small Intestine	intestine
15	chr15:57599600-57617800	Weak transcription	Spleen	Spleen
16	chr15:57599800-57603000	Strong transcription	Primary B cells from cord blood	blood
17	chr15:57600000-57604400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr15:57600200-57603000	Weak transcription	Stomach Mucosa	stomach
19	chr15:57600200-57604400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:57600200-57605000	Weak transcription	Fetal Kidney	kidney
21	chr15:57600600-57604200	Weak transcription	Fetal Lung	lung
22	chr15:57600800-57603800	Weak transcription	HepG2	liver
23	chr15:57601400-57603000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:57601400-57605200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:57602000-57605600	Enhancers	Fetal Stomach	stomach
26	chr15:57602000-57605800	Enhancers	Fetal Muscle Trunk	muscle
27	chr15:57602000-57606800	Enhancers	Fetal Intestine Large	intestine
28	chr15:57602400-57604000	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr15:57602400-57604800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:57602400-57605000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr15:57602400-57606800	Enhancers	Fetal Intestine Small	intestine
32	chr15:57602400-57607200	Enhancers	Fetal Muscle Leg	muscle
33	chr15:57602600-57603000	Enhancers	Brain Germinal Matrix	brain
34	chr15:57602600-57603200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr15:57602600-57604000	Enhancers	Gastric	stomach
36	chr15:57602600-57604600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr15:57602800-57603200	Weak transcription	Placenta	Placenta
38	chr15:57602800-57617000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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