Variant report

Variant	rs678466
Chromosome Location	chr1:47116718-47116719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10890410	0.85[ASN][1000 genomes]
rs10890414	0.82[ASN][1000 genomes]
rs11211332	0.89[EUR][1000 genomes]
rs11211343	0.82[ASN][1000 genomes]
rs11801744	0.82[ASN][1000 genomes]
rs12562113	0.81[ASN][1000 genomes]
rs12566278	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12568734	0.82[ASN][1000 genomes]
rs1258055	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1258058	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1258063	0.92[ASN][1000 genomes]
rs1258064	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1258065	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1258066	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1258068	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1258072	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1268714	0.94[ASN][1000 genomes]
rs1273237	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13374909	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1745376	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1933932	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2146560	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2181412	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241863	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2241864	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2439442	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2476153	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2476155	0.95[ASN][1000 genomes]
rs2476156	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2476157	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2476159	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2486160	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2486162	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011290	0.87[ASN][1000 genomes]
rs3766218	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3766220	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3766221	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3766222	0.85[ASN][1000 genomes]
rs3766223	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56771521	0.82[ASN][1000 genomes]
rs57495753	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs582269	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs582323	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs582760	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs583649	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58678760	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59479990	0.82[ASN][1000 genomes]
rs596794	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs597221	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs604233	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs604264	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs611919	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs629412	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs631368	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs631840	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs636082	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs636122	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs636424	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs648822	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs654544	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs655369	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs657166	0.89[ASN][1000 genomes]
rs669647	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs673134	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs675731	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs683585	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs685862	0.84[AMR][1000 genomes]
rs689300	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs723333	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs724309	0.84[ASN][1000 genomes]
rs72896683	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72900715	0.82[ASN][1000 genomes]
rs736188	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9094	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1007280	chr1:47088116-47129588	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47088200-47131600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:47090200-47121400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:47094600-47119200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:47101600-47130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:47101600-47133000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:47101800-47119000	Weak transcription	Colonic Mucosa	Colon
7	chr1:47101800-47121200	Weak transcription	HUVEC	blood vessel
8	chr1:47102000-47122400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:47102400-47121400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:47103000-47132800	Weak transcription	Spleen	Spleen
11	chr1:47105000-47132800	Weak transcription	Stomach Mucosa	stomach
12	chr1:47108200-47123400	Weak transcription	K562	blood
13	chr1:47109400-47129800	Weak transcription	Pancreas	Pancrea
14	chr1:47109400-47132600	Weak transcription	Hela-S3	cervix
15	chr1:47109600-47123400	Weak transcription	NH-A	brain
16	chr1:47109600-47132600	Weak transcription	HMEC	breast
17	chr1:47109800-47123200	Weak transcription	HepG2	liver
18	chr1:47112200-47125600	Strong transcription	Liver	Liver
19	chr1:47112400-47126800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:47112600-47116800	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:47112800-47116800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:47112800-47125400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:47112800-47125800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:47113000-47124400	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr1:47113600-47121800	Weak transcription	NHEK	skin
26	chr1:47113800-47118400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:47114600-47116800	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr1:47114600-47124600	Strong transcription	Fetal Thymus	thymus
29	chr1:47115000-47116800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:47115000-47116800	Strong transcription	Osteobl	bone
31	chr1:47115000-47125200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:47115000-47125400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:47115200-47116800	Strong transcription	Fetal Brain Male	brain
34	chr1:47115400-47124200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:47115600-47119000	Weak transcription	NHLF	lung
36	chr1:47115600-47133000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:47115800-47121600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:47115800-47121800	Weak transcription	Psoas Muscle	Psoas
39	chr1:47115800-47132000	Weak transcription	Fetal Heart	heart
40	chr1:47116000-47118000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:47116000-47118800	Weak transcription	Fetal Intestine Small	intestine
42	chr1:47116000-47119000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:47116000-47119000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr1:47116000-47120400	Weak transcription	Gastric	stomach
45	chr1:47116000-47120600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:47116000-47121400	Weak transcription	Dnd41	blood
47	chr1:47116000-47121600	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:47116000-47121800	Weak transcription	Right Ventricle	heart
49	chr1:47116000-47123800	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr1:47116000-47127400	Weak transcription	Fetal Stomach	stomach

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