Variant report

Variant	rs3770391
Chromosome Location	chr2:53991222-53991223
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR75-2	chr2:53990098-53992017	NONHSAT070699

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10204047	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10204432	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10490472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10490473	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13387421	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13404007	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13426962	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17039534	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17045069	0.83[AMR][1000 genomes]
rs17045109	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17045123	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17045139	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17045239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17045241	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17045262	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17045286	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17045296	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2056650	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2287339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2287346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2287347	0.95[CHB][hapmap];0.85[ASN][1000 genomes]
rs2302876	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2302880	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28834518	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3213768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3213774	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3755113	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3755114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs3755119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3815650	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3821079	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59951261	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60972886	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6545368	0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs6724214	0.87[ASN][1000 genomes]
rs6761242	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72799242	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72799275	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72901302	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72902916	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72902923	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72902926	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72902929	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7601553	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7605552	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs997643	0.83[AMR][1000 genomes]

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	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
3	chr2:53937000-53994400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:53937200-53994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:53937400-53994400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:53938400-53992400	Weak transcription	K562	blood
7	chr2:53958200-53994400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:53963000-53994000	Weak transcription	A549	lung
9	chr2:53973400-53994400	Weak transcription	Colonic Mucosa	Colon
10	chr2:53975800-53994400	Weak transcription	Fetal Kidney	kidney
11	chr2:53978800-53994200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:53979400-53994000	Weak transcription	Osteobl	bone
13	chr2:53979800-53994200	Weak transcription	Psoas Muscle	Psoas
14	chr2:53979800-53994200	Weak transcription	NHLF	lung
15	chr2:53982400-53991600	Weak transcription	Stomach Mucosa	stomach
16	chr2:53982400-53991800	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:53982400-53994400	Weak transcription	NHDF-Ad	bronchial
18	chr2:53982800-53994000	Weak transcription	HMEC	breast
19	chr2:53982800-53994200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:53983000-53994000	Weak transcription	Small Intestine	intestine
21	chr2:53983200-53993200	Strong transcription	Primary T cells from cord blood	blood
22	chr2:53984200-53992800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:53984200-53993000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:53984200-53994200	Weak transcription	HSMMtube	muscle
25	chr2:53984200-53994400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:53984200-53994400	Weak transcription	Lung	lung
27	chr2:53984200-53994400	Weak transcription	Right Ventricle	heart
28	chr2:53984400-53992400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:53984600-53994400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:53984800-53994200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:53984800-53994400	Weak transcription	Brain Angular Gyrus	brain
32	chr2:53986400-53994000	Weak transcription	Brain Germinal Matrix	brain
33	chr2:53986400-53994000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr2:53986400-53994600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:53987000-53992400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:53987200-53994400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:53987400-53991600	Strong transcription	Liver	Liver
38	chr2:53987400-53991800	Strong transcription	Primary hematopoietic stem cells	blood
39	chr2:53987800-53991400	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr2:53987800-53992800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr2:53988200-53992400	Strong transcription	HepG2	liver
42	chr2:53988400-53992000	Strong transcription	Fetal Muscle Leg	muscle
43	chr2:53988400-53992400	Strong transcription	Primary B cells from cord blood	blood
44	chr2:53988400-53992800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:53988600-53991800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:53988600-53991800	Strong transcription	Dnd41	blood
47	chr2:53988600-53992000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr2:53988600-53992400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr2:53988600-53992400	Strong transcription	GM12878-XiMat	blood
50	chr2:53988600-53993000	Strong transcription	Fetal Thymus	thymus

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