Variant report

Variant	rs10899078
Chromosome Location	chr11:74862866-74862867
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74860499..74862617-chr11:74862814..74864502,2	K562	blood:

Variant related genes	Relation type
ENSG00000137491	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10793114	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10899076	0.95[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10899077	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899079	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs11236348	0.93[CEU][hapmap];0.85[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11236349	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11236350	0.95[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11236351	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11236352	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11236353	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11236354	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11236356	0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap]
rs11236357	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11236361	0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11236365	0.86[CEU][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs11822379	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12361277	0.86[AMR][1000 genomes]
rs12422149	0.95[JPT][hapmap]
rs3740839	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4100076	0.82[CHB][hapmap];0.85[CHD][hapmap];0.92[MEX][hapmap];0.92[AMR][1000 genomes]
rs4397881	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4944073	0.85[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4944074	0.95[CEU][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes]
rs4944975	0.90[CEU][hapmap];0.90[TSI][hapmap]
rs4944990	0.95[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4944991	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4944992	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944993	0.91[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4944994	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57073688	0.81[ASN][1000 genomes]
rs59633704	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67904312	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs67947132	0.90[AMR][1000 genomes]
rs7125268	0.86[CEU][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs72996586	0.92[AMR][1000 genomes]
rs72998525	0.84[AMR][1000 genomes]
rs881217	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs949069	0.90[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897919	chr11:74862391-74875501	Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10899078	PDE2A	cis	parietal	SCAN
rs10899078	UVRAG	cis	parietal	SCAN
rs10899078	FCHSD2	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74856600-74863400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:74857400-74865600	Weak transcription	Small Intestine	intestine
3	chr11:74859000-74863800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:74859200-74863200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:74860000-74864000	Weak transcription	Spleen	Spleen
6	chr11:74861200-74863600	Enhancers	Gastric	stomach
7	chr11:74861200-74868400	Active TSS	Brain Hippocampus Middle	brain
8	chr11:74861400-74864000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
9	chr11:74861400-74866000	Active TSS	Brain Anterior Caudate	brain
10	chr11:74861600-74864800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
11	chr11:74861600-74866200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:74861600-74867200	Active TSS	Brain Cingulate Gyrus	brain
13	chr11:74861800-74863200	Enhancers	Fetal Muscle Trunk	muscle
14	chr11:74861800-74864600	Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr11:74861800-74864800	Active TSS	Rectal Smooth Muscle	rectum
16	chr11:74862000-74863000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:74862000-74863000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:74862000-74864600	Active TSS	Psoas Muscle	Psoas
19	chr11:74862000-74864800	Flanking Active TSS	Fetal Intestine Large	intestine
20	chr11:74862000-74864800	Flanking Active TSS	Fetal Muscle Leg	muscle
21	chr11:74862000-74864800	Flanking Active TSS	HepG2	liver
22	chr11:74862000-74865000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr11:74862000-74865200	Active TSS	Adipose Nuclei	Adipose
24	chr11:74862200-74863000	Active TSS	Placenta	Placenta
25	chr11:74862200-74863200	Flanking Active TSS	Esophagus	oesophagus
26	chr11:74862200-74864400	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr11:74862200-74864400	Flanking Active TSS	Fetal Intestine Small	intestine
28	chr11:74862200-74864400	Active TSS	Ovary	ovary
29	chr11:74862200-74864800	Active TSS	Brain Angular Gyrus	brain
30	chr11:74862200-74864800	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr11:74862200-74864800	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr11:74862200-74864800	Active TSS	Lung	lung
33	chr11:74862200-74865000	Active TSS	Right Atrium	heart
34	chr11:74862200-74866000	Active TSS	Brain Substantia Nigra	brain
35	chr11:74862400-74863000	Weak transcription	Fetal Thymus	thymus
36	chr11:74862400-74863600	Active TSS	Colon Smooth Muscle	Colon
37	chr11:74862400-74864600	Flanking Active TSS	Liver	Liver
38	chr11:74862600-74863000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:74862600-74863400	Active TSS	Pancreas	Pancrea
40	chr11:74862600-74863600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:74862600-74864400	Active TSS	Left Ventricle	heart
42	chr11:74862600-74865000	Enhancers	Stomach Mucosa	stomach
43	chr11:74862800-74863000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
44	chr11:74862800-74863200	Flanking Active TSS	Colonic Mucosa	Colon
45	chr11:74862800-74863200	Enhancers	Fetal Stomach	stomach
46	chr11:74862800-74863400	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr11:74862800-74864800	Flanking Active TSS	Right Ventricle	heart

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