Variant report

Variant	rs1569579
Chromosome Location	chr6:24513636-24513637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24513157..24516744-chr6:24716201..24720680,4	K562	blood:

Variant related genes	Relation type
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2010190	0.82[CHB][hapmap]
rs2744572	0.82[CHB][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs2744588	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2744593	0.81[AMR][1000 genomes]
rs2744594	0.86[MEX][hapmap]
rs2744597	0.82[MEX][hapmap]
rs2760137	0.80[EUR][1000 genomes]
rs2760138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2817226	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2817229	0.85[ASN][1000 genomes]
rs807512	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs807513	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs807515	0.81[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs807519	0.86[MEX][hapmap]
rs807527	0.81[MEX][hapmap]
rs807531	0.82[MEX][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	esv2763542	chr6:24445131-24520637	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv519552	chr6:24451256-24524704	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv34020	chr6:24481299-24606036	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1569579	GPLD1	cis	Thyroid	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24495800-24517800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:24496000-24517800	Weak transcription	Spleen	Spleen
3	chr6:24496000-24534200	Weak transcription	Gastric	stomach
4	chr6:24496000-24538000	Weak transcription	Esophagus	oesophagus
5	chr6:24496200-24526400	Weak transcription	Right Atrium	heart
6	chr6:24496200-24527800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:24496200-24534200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:24496200-24535000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr6:24496200-24536200	Weak transcription	Psoas Muscle	Psoas
10	chr6:24496200-24583000	Weak transcription	Hela-S3	cervix
11	chr6:24496400-24517200	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:24496400-24532200	Weak transcription	Brain Germinal Matrix	brain
13	chr6:24496800-24517600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr6:24496800-24522800	Weak transcription	Lung	lung
15	chr6:24496800-24532400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:24497000-24528200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr6:24497400-24522400	Weak transcription	K562	blood
18	chr6:24498400-24517400	Weak transcription	GM12878-XiMat	blood
19	chr6:24498800-24517600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:24504200-24513800	Weak transcription	Aorta	Aorta
21	chr6:24504200-24522600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:24504400-24534200	Weak transcription	Pancreas	Pancrea
23	chr6:24505200-24516800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:24505400-24534000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:24505600-24516000	Weak transcription	A549	lung
26	chr6:24505800-24527800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:24505800-24530800	Weak transcription	Right Ventricle	heart
28	chr6:24505800-24534000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:24505800-24534000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr6:24506400-24513800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr6:24506400-24514000	Weak transcription	Ovary	ovary
32	chr6:24506400-24530000	Weak transcription	Placenta	Placenta
33	chr6:24506800-24518000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:24507400-24513800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:24507400-24513800	Weak transcription	Fetal Intestine Large	intestine
36	chr6:24507400-24531400	Weak transcription	Fetal Lung	lung
37	chr6:24507600-24514000	Weak transcription	Brain Angular Gyrus	brain
38	chr6:24507600-24514200	Weak transcription	Brain Anterior Caudate	brain
39	chr6:24507600-24522800	Weak transcription	Fetal Kidney	kidney
40	chr6:24507600-24532400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr6:24507600-24532400	Weak transcription	Fetal Brain Female	brain
42	chr6:24507800-24513800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr6:24507800-24532400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr6:24507800-24536800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr6:24507800-24539200	Weak transcription	Brain Hippocampus Middle	brain
46	chr6:24508000-24515400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:24508000-24515400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:24508000-24521000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:24508800-24514000	Weak transcription	Primary B cells from cord blood	blood
50	chr6:24509400-24545800	Weak transcription	Small Intestine	intestine

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