Variant report

Variant	rs2248014
Chromosome Location	chr8:99030280-99030281
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1466428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1965914	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2034779	0.90[JPT][hapmap]
rs2255464	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2444860	0.85[MEX][hapmap]
rs2444873	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2444892	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2513809	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2513810	0.91[ASN][1000 genomes]
rs2513811	0.98[ASN][1000 genomes]
rs2513852	0.85[CHD][hapmap];0.85[MEX][hapmap]
rs2615	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2248014	GRHL2	cis	parietal	SCAN
rs2248014	LAPTM4B	cis	lymphoblastoid	seeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99008400-99045000	Weak transcription	Colonic Mucosa	Colon
2	chr8:99012000-99032000	Weak transcription	Gastric	stomach
3	chr8:99015000-99034400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr8:99019000-99033200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr8:99020000-99033400	Weak transcription	Left Ventricle	heart
6	chr8:99021000-99032200	Weak transcription	Brain Substantia Nigra	brain
7	chr8:99021200-99032800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr8:99021200-99053600	Weak transcription	A549	lung
9	chr8:99021400-99033400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr8:99021400-99043800	Weak transcription	Brain Germinal Matrix	brain
11	chr8:99022400-99055200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr8:99023000-99033400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr8:99023600-99034800	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr8:99023800-99041200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:99024000-99032800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr8:99024000-99044000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr8:99024000-99054800	Weak transcription	Right Ventricle	heart
18	chr8:99024200-99032800	Weak transcription	Colon Smooth Muscle	Colon
19	chr8:99024200-99033200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr8:99024200-99033200	Weak transcription	NHDF-Ad	bronchial
21	chr8:99024200-99033600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr8:99024200-99042800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr8:99024200-99055000	Weak transcription	Fetal Brain Male	brain
24	chr8:99024200-99056000	Weak transcription	Spleen	Spleen
25	chr8:99024400-99032800	Weak transcription	HSMMtube	muscle
26	chr8:99025000-99030600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr8:99025000-99052800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr8:99025200-99045400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr8:99025400-99032600	Strong transcription	Fetal Stomach	stomach
30	chr8:99025400-99045200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr8:99026000-99033200	Weak transcription	NHLF	lung
32	chr8:99026800-99033400	Weak transcription	Small Intestine	intestine
33	chr8:99026800-99036600	Weak transcription	Lung	lung
34	chr8:99027200-99031000	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr8:99027200-99031400	Weak transcription	Dnd41	blood
36	chr8:99027400-99032200	Strong transcription	Fetal Muscle Leg	muscle
37	chr8:99027600-99037400	Weak transcription	Primary B cells from peripheral blood	blood
38	chr8:99027600-99045400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr8:99027800-99032800	Weak transcription	Fetal Heart	heart
40	chr8:99028000-99030600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr8:99028200-99032400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr8:99028400-99033400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr8:99028600-99032000	Strong transcription	Ovary	ovary
44	chr8:99028800-99030400	Strong transcription	Adipose Nuclei	Adipose
45	chr8:99028800-99030400	Strong transcription	Osteobl	bone
46	chr8:99028800-99030600	Strong transcription	Aorta	Aorta
47	chr8:99028800-99030800	Strong transcription	Stomach Smooth Muscle	stomach
48	chr8:99028800-99032000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr8:99028800-99045400	Weak transcription	Fetal Brain Female	brain
50	chr8:99029000-99032600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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