Variant report

Variant	rs1777274
Chromosome Location	chr1:57004147-57004148
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRKAA2-9	chr1:57004124-57004583	NONHSAT003451

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10888977	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11206833	0.83[EUR][1000 genomes]
rs12082242	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1759750	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1759752	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1777277	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1810930	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1930760	0.85[AFR][1000 genomes]
rs1930762	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4532850	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4912377	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs55798508	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7529520	0.90[EUR][1000 genomes]
rs7535757	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7556056	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs953856	0.83[AFR][1000 genomes]
rs993075	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv945965	chr1:57003085-57005467	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56987000-57015000	Genic enhancers	NHDF-Ad	bronchial
2	chr1:56992800-57011200	Weak transcription	Stomach Mucosa	stomach
3	chr1:56993000-57004600	Weak transcription	Hela-S3	cervix
4	chr1:56993600-57007800	Weak transcription	Primary B cells from cord blood	blood
5	chr1:56993800-57004200	Weak transcription	NH-A	brain
6	chr1:56994000-57012400	Weak transcription	Fetal Brain Male	brain
7	chr1:56994000-57012800	Weak transcription	Fetal Brain Female	brain
8	chr1:56994200-57004400	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr1:56995600-57004600	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:56996600-57005200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:56997200-57004600	Genic enhancers	Placenta	Placenta
12	chr1:56997600-57004400	Genic enhancers	Fetal Muscle Leg	muscle
13	chr1:56999400-57012800	Weak transcription	HSMMtube	muscle
14	chr1:57000000-57004200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr1:57000200-57005000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:57000200-57008200	Weak transcription	Fetal Kidney	kidney
17	chr1:57000400-57011000	Weak transcription	Gastric	stomach
18	chr1:57000400-57013000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:57000600-57005400	Weak transcription	Colonic Mucosa	Colon
20	chr1:57001000-57004200	Enhancers	Pancreas	Pancrea
21	chr1:57001200-57018800	Weak transcription	A549	lung
22	chr1:57001400-57004600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:57001800-57018600	Weak transcription	Small Intestine	intestine
24	chr1:57001800-57021800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:57002200-57004400	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:57002200-57004400	Enhancers	Psoas Muscle	Psoas
27	chr1:57002400-57004600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:57002400-57005200	Weak transcription	Aorta	Aorta
29	chr1:57002400-57008600	Enhancers	Brain Hippocampus Middle	brain
30	chr1:57002600-57004600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:57002600-57005200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:57002600-57005200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:57002600-57006600	Enhancers	Right Atrium	heart
34	chr1:57002600-57008600	Enhancers	Brain Anterior Caudate	brain
35	chr1:57002800-57004200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:57002800-57004200	Enhancers	Right Ventricle	heart
37	chr1:57002800-57004200	Enhancers	Dnd41	blood
38	chr1:57002800-57004400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:57002800-57004400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:57002800-57004600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr1:57002800-57004800	Weak transcription	Fetal Heart	heart
42	chr1:57002800-57006400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:57002800-57006600	Enhancers	H9 Cell Line	embryonic stem cell
44	chr1:57002800-57006800	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr1:57002800-57006800	Enhancers	Fetal Intestine Small	intestine
46	chr1:57002800-57013200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:57002800-57018600	Weak transcription	Thymus	Thymus
48	chr1:57003000-57004200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:57003000-57004600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:57003000-57005000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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