Variant report

Variant	rs669647
Chromosome Location	chr1:47142475-47142476
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr1:47141509-47142753	PBDE	blood:	n/a	n/a
2	IRF1	chr1:47142058-47142555	K562	blood:	n/a	n/a
3	IRF1	chr1:47141182-47142625	K562	blood:	n/a	chr1:47141620-47141641

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:47141770..47144692-chr1:47177130..47178944,2	K562	blood:
2	chr1:47132879..47135178-chr1:47141656..47143766,2	MCF-7	breast:
3	chr1:47130612..47137538-chr1:47138503..47143012,9	K562	blood:
4	chr1:47134378..47137611-chr1:47139710..47142903,4	MCF-7	breast:
5	chr1:47136300..47139021-chr1:47142409..47144018,2	MCF-7	breast:
6	chr1:47141197..47146499-chr1:47148014..47152846,8	K562	blood:

No data

Variant related genes	Relation type
ATPAF1	TF binding region
ENSG00000233647	Chromatin interaction
ENSG00000159658	Chromatin interaction
ENSG00000123472	Chromatin interaction
ENSG00000186118	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10890410	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs10890414	0.97[ASN][1000 genomes]
rs11211332	0.89[EUR][1000 genomes]
rs11211343	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11211347	0.86[ASN][1000 genomes]
rs11801744	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12059860	1.00[CEU][hapmap]
rs12060032	0.83[ASN][1000 genomes]
rs12562113	0.88[ASN][1000 genomes]
rs12566278	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12568734	0.97[ASN][1000 genomes]
rs1258010	1.00[TSI][hapmap]
rs1258022	1.00[TSI][hapmap]
rs1258055	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1258058	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258063	0.86[ASN][1000 genomes]
rs1258064	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258065	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258066	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258068	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258072	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1268714	0.88[ASN][1000 genomes]
rs1273237	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13374909	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1745376	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1933932	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2146560	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2181412	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2241863	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241864	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439442	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2476153	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2476155	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2476156	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2476157	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2476159	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2486160	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2486162	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3011290	0.89[ASN][1000 genomes]
rs3766218	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766220	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766221	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766222	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3766223	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56771521	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs57495753	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs582269	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs582323	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs582760	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs583649	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58678760	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58920789	0.83[ASN][1000 genomes]
rs59479990	0.97[ASN][1000 genomes]
rs596794	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs597221	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60239027	0.83[ASN][1000 genomes]
rs604233	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs604264	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs611919	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs629412	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs631368	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs631840	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs636082	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs636122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs636424	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs648822	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs654544	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs655369	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs657166	0.96[ASN][1000 genomes]
rs6677350	1.00[CEU][hapmap]
rs673134	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs675731	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs678466	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs683585	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs685862	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes]
rs689300	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs723333	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs724309	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs72896683	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72900715	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs736188	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9094	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	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	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47134400-47145800	Weak transcription	Hela-S3	cervix
2	chr1:47134400-47147800	Weak transcription	Small Intestine	intestine
3	chr1:47134600-47142600	Weak transcription	HSMMtube	muscle
4	chr1:47134600-47142800	Weak transcription	Ovary	ovary
5	chr1:47134600-47143000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:47134600-47143200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:47134600-47145600	Weak transcription	Fetal Kidney	kidney
8	chr1:47134600-47145800	Weak transcription	Fetal Brain Male	brain
9	chr1:47134600-47147000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:47134600-47147800	Weak transcription	Psoas Muscle	Psoas
11	chr1:47134600-47149200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:47134600-47153000	Weak transcription	Right Atrium	heart
13	chr1:47134600-47157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:47134800-47142800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:47134800-47142800	Weak transcription	Fetal Lung	lung
16	chr1:47134800-47143000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:47134800-47143200	Weak transcription	Brain Angular Gyrus	brain
18	chr1:47134800-47152600	Weak transcription	A549	lung
19	chr1:47135000-47145400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:47135000-47145400	Weak transcription	Esophagus	oesophagus
21	chr1:47138000-47152000	Strong transcription	Stomach Smooth Muscle	stomach
22	chr1:47138000-47157800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:47138200-47147600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:47138200-47152200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:47138200-47152600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:47138200-47159400	Strong transcription	Placenta	Placenta
27	chr1:47138400-47147800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:47138400-47151600	Strong transcription	Duodenum Mucosa	Duodenum
29	chr1:47138400-47152200	Strong transcription	Adipose Nuclei	Adipose
30	chr1:47138400-47158800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr1:47138400-47159400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:47138600-47152400	Strong transcription	Primary hematopoietic stem cells	blood
33	chr1:47138800-47143600	Strong transcription	Pancreas	Pancrea
34	chr1:47138800-47152800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr1:47138800-47153200	Strong transcription	Fetal Muscle Leg	muscle
36	chr1:47138800-47158600	Strong transcription	Primary B cells from cord blood	blood
37	chr1:47139000-47142800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr1:47139000-47145800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:47139000-47148400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:47139000-47152400	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:47139000-47152800	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:47139000-47159400	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr1:47139200-47145200	Weak transcription	Gastric	stomach
44	chr1:47139200-47147400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:47139200-47153000	Weak transcription	Fetal Heart	heart
46	chr1:47139200-47153400	Strong transcription	Dnd41	blood
47	chr1:47139200-47159400	Strong transcription	Brain Germinal Matrix	brain
48	chr1:47139200-47159800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:47139400-47146800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr1:47139400-47152600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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