Variant report

Variant	rs2654947
Chromosome Location	chr4:148579490-148579491
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	chr4:148578289..148581329-chr4:148601493..148604783,3	K562	blood:

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10012122	1.00[TSI][hapmap]
rs10305875	1.00[MEX][hapmap]
rs10519914	1.00[TSI][hapmap]
rs11934646	0.82[AFR][1000 genomes]
rs11939191	1.00[TSI][hapmap]
rs1517135	1.00[TSI][hapmap]
rs17023959	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2036502	0.90[AFR][1000 genomes]
rs2718451	0.82[AFR][1000 genomes]
rs6535547	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs6535551	0.91[YRI][hapmap]
rs9308221	1.00[TSI][hapmap]
rs931779	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9997823	1.00[TSI][hapmap]
rs9999853	1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830110	chr4:148432125-148595119	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv428776	chr4:148432125-148595119	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2654947	GRM3	trans	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148548400-148599800	Weak transcription	Gastric	stomach
2	chr4:148548600-148604400	Weak transcription	Esophagus	oesophagus
3	chr4:148549000-148599800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:148551400-148603600	Weak transcription	Hela-S3	cervix
5	chr4:148554600-148604600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:148556000-148581000	Weak transcription	Brain Angular Gyrus	brain
7	chr4:148556000-148603800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:148556400-148599600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:148556600-148595200	Weak transcription	NHLF	lung
10	chr4:148557400-148603800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:148557600-148594000	Weak transcription	NHEK	skin
12	chr4:148557800-148603800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:148558200-148603800	Weak transcription	A549	lung
14	chr4:148558400-148603800	Weak transcription	HUVEC	blood vessel
15	chr4:148559400-148599200	Weak transcription	HMEC	breast
16	chr4:148561200-148596200	Weak transcription	NHDF-Ad	bronchial
17	chr4:148562400-148581000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr4:148562800-148585000	Weak transcription	Fetal Brain Male	brain
19	chr4:148562800-148603800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:148562800-148604200	Weak transcription	Right Ventricle	heart
21	chr4:148563600-148604400	Weak transcription	Pancreas	Pancrea
22	chr4:148563800-148599800	Weak transcription	Spleen	Spleen
23	chr4:148565000-148602200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr4:148568400-148582400	Weak transcription	Stomach Mucosa	stomach
25	chr4:148568400-148603800	Weak transcription	Fetal Kidney	kidney
26	chr4:148568800-148584000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:148568800-148600400	Weak transcription	Psoas Muscle	Psoas
28	chr4:148569000-148580000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr4:148569400-148604000	Weak transcription	Brain Hippocampus Middle	brain
30	chr4:148570200-148599400	Weak transcription	K562	blood
31	chr4:148570400-148595800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:148570400-148604200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:148570800-148583200	Weak transcription	Fetal Heart	heart
34	chr4:148571600-148603800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:148572800-148585600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:148573200-148582400	Strong transcription	Fetal Thymus	thymus
37	chr4:148573800-148587200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr4:148574000-148579600	Strong transcription	Dnd41	blood
39	chr4:148574000-148580200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:148574000-148582800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr4:148574000-148584000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr4:148574000-148589800	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr4:148574200-148580000	Strong transcription	Primary B cells from cord blood	blood
44	chr4:148574200-148581600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr4:148574200-148582000	Strong transcription	Adipose Nuclei	Adipose
46	chr4:148574200-148582200	Strong transcription	Fetal Intestine Large	intestine
47	chr4:148574200-148584000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr4:148574200-148584200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:148574600-148596800	Strong transcription	Primary T cells from cord blood	blood
50	chr4:148574800-148579800	Strong transcription	Rectal Mucosa Donor 29	rectum

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