Variant report

Variant	rs655369
Chromosome Location	chr1:47127381-47127382
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:47127312-47127410	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:47126136..47128149-chr1:47129414..47131202,2	K562	blood:
2	chr1:47127093..47130173-chr1:47131972..47135194,3	K562	blood:
3	chr1:47126136..47129004-chr1:47129301..47131202,4	K562	blood:
4	chr1:47124455..47128063-chr1:47131072..47135010,3	MCF-7	breast:
5	chr1:47125032..47127467-chr1:47178869..47180403,2	K562	blood:

Variant related genes	Relation type
ATPAF1	TF binding region
ENSG00000233647	Chromatin interaction
ENSG00000186118	Chromatin interaction
ENSG00000123472	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10890410	0.96[ASN][1000 genomes]
rs10890414	0.93[ASN][1000 genomes]
rs11211332	0.89[EUR][1000 genomes]
rs11211343	0.93[ASN][1000 genomes]
rs11211347	0.82[ASN][1000 genomes]
rs11801744	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12562113	0.92[ASN][1000 genomes]
rs12566278	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12568734	0.93[ASN][1000 genomes]
rs1258055	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1258058	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1258063	0.90[ASN][1000 genomes]
rs1258064	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1258065	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1258066	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1258068	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1258072	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1268714	0.92[ASN][1000 genomes]
rs1273237	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13374909	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1745376	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1933932	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2146560	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2181412	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241863	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2241864	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2439442	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476153	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2476155	0.92[ASN][1000 genomes]
rs2476156	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2476157	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2476159	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2486160	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2486162	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3011290	0.93[ASN][1000 genomes]
rs3766218	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766220	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3766221	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766222	0.96[ASN][1000 genomes]
rs3766223	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56771521	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs57495753	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs582269	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs582323	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs582760	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58678760	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59479990	0.93[ASN][1000 genomes]
rs596794	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597221	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604233	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs604264	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs611919	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629412	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631368	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631840	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs636082	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636122	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs636424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648822	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs654544	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs657166	1.00[ASN][1000 genomes]
rs669647	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs673134	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs675731	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs678466	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs683585	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs685862	0.95[AMR][1000 genomes]
rs689300	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723333	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs724309	0.81[ASN][1000 genomes]
rs72896683	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72900715	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs736188	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9094	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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:125 , 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	chr1:47101600-47130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:47101600-47133000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:47103000-47132800	Weak transcription	Spleen	Spleen
5	chr1:47105000-47132800	Weak transcription	Stomach Mucosa	stomach
6	chr1:47109400-47129800	Weak transcription	Pancreas	Pancrea
7	chr1:47109400-47132600	Weak transcription	Hela-S3	cervix
8	chr1:47109600-47132600	Weak transcription	HMEC	breast
9	chr1:47115600-47133000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:47115800-47132000	Weak transcription	Fetal Heart	heart
11	chr1:47116000-47127400	Weak transcription	Fetal Stomach	stomach
12	chr1:47116000-47130000	Weak transcription	Lung	lung
13	chr1:47116000-47130600	Weak transcription	Esophagus	oesophagus
14	chr1:47116000-47131800	Weak transcription	Aorta	Aorta
15	chr1:47116600-47130000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:47116600-47131400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:47117600-47127600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:47117600-47127600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:47118000-47132800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:47118200-47130000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:47119000-47132400	Weak transcription	A549	lung
22	chr1:47119200-47132400	Weak transcription	Small Intestine	intestine
23	chr1:47120000-47127400	Weak transcription	Fetal Intestine Small	intestine
24	chr1:47121000-47129400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:47121000-47133000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:47122000-47129800	Weak transcription	Colonic Mucosa	Colon
27	chr1:47122000-47130000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:47122200-47130000	Weak transcription	NHEK	skin
29	chr1:47122200-47131000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:47122400-47132000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:47122600-47132200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:47122600-47133000	Weak transcription	Gastric	stomach
33	chr1:47122800-47129200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:47122800-47129400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:47122800-47129400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:47122800-47130000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:47122800-47130000	Weak transcription	Brain Germinal Matrix	brain
38	chr1:47122800-47130000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:47122800-47132000	Weak transcription	NHLF	lung
40	chr1:47122800-47132200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:47123000-47129800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:47123600-47129400	Weak transcription	Fetal Brain Female	brain
43	chr1:47123600-47129800	Weak transcription	NHDF-Ad	bronchial
44	chr1:47123600-47131400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr1:47123600-47132600	Weak transcription	HUVEC	blood vessel
46	chr1:47123600-47133000	Weak transcription	HSMMtube	muscle
47	chr1:47123800-47129400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:47123800-47129800	Weak transcription	K562	blood
49	chr1:47123800-47130000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr1:47123800-47130000	Weak transcription	Brain Substantia Nigra	brain

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