Variant report

Variant	rs2252525
Chromosome Location	chr6:24514569-24514570
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24504155..24505791-chr6:24513770..24515648,2	K562	blood:
2	chr6:24513157..24516744-chr6:24716201..24720680,4	K562	blood:

Variant related genes	Relation type
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2760136	0.81[ASN][1000 genomes]
rs2817229	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs807512	0.81[AMR][1000 genomes]
rs807515	0.87[ASW][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[MEX][hapmap];0.84[AFR][1000 genomes];0.90[AMR][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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2252525	HIST1H4H	cis	parietal	SCAN
rs2252525	HIST1H3A	cis	cerebellum	SCAN
rs2252525	ZKSCAN4	cis	parietal	SCAN
rs2252525	ABT1	cis	cerebellum	SCAN

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	chr6:24504200-24522600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:24504400-24534200	Weak transcription	Pancreas	Pancrea
22	chr6:24505200-24516800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:24505400-24534000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:24505600-24516000	Weak transcription	A549	lung
25	chr6:24505800-24527800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr6:24505800-24530800	Weak transcription	Right Ventricle	heart
27	chr6:24505800-24534000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:24505800-24534000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr6:24506400-24530000	Weak transcription	Placenta	Placenta
30	chr6:24506800-24518000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:24507400-24531400	Weak transcription	Fetal Lung	lung
32	chr6:24507600-24522800	Weak transcription	Fetal Kidney	kidney
33	chr6:24507600-24532400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr6:24507600-24532400	Weak transcription	Fetal Brain Female	brain
35	chr6:24507800-24532400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:24507800-24536800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr6:24507800-24539200	Weak transcription	Brain Hippocampus Middle	brain
38	chr6:24508000-24515400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:24508000-24515400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr6:24508000-24521000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr6:24509400-24545800	Weak transcription	Small Intestine	intestine
42	chr6:24509800-24516600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr6:24511600-24518800	Strong transcription	HepG2	liver
44	chr6:24511800-24516800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:24512200-24516000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:24512200-24516200	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr6:24512200-24521000	Strong transcription	Liver	Liver
48	chr6:24512200-24521400	Strong transcription	Dnd41	blood
49	chr6:24512200-24525000	Strong transcription	Fetal Intestine Small	intestine
50	chr6:24512400-24514800	Strong transcription	Duodenum Mucosa	Duodenum

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