Variant report

Variant	rs58678760
Chromosome Location	chr1:47153538-47153539
allele	A/C
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	MEF2A	chr1:47152993-47153576	SK-N-SH	brain:	n/a	chr1:47153272-47153287 chr1:47153272-47153286 chr1:47153270-47153291 chr1:47153275-47153284 chr1:47153270-47153291 chr1:47153332-47153353 chr1:47153274-47153285 chr1:47153271-47153287 chr1:47153273-47153284
2	NFIC	chr1:47152821-47153538	SK-N-SH	brain:	n/a	chr1:47153133-47153150 chr1:47153134-47153150

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47131372..47133587-chr1:47151853..47154733,2	MCF-7	breast:
2	chr1:47151853..47154363-chr1:47155084..47157704,2	K562	blood:

Variant related genes	Relation type
EFCAB14	TF binding region
ENSG00000159658	Chromatin interaction
ENSG00000233647	Chromatin interaction
ENSG00000123472	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10890410	1.00[ASN][1000 genomes]
rs10890414	0.97[ASN][1000 genomes]
rs11211332	1.00[EUR][1000 genomes]
rs11211343	0.97[ASN][1000 genomes]
rs11211347	0.86[ASN][1000 genomes]
rs11801744	0.97[ASN][1000 genomes]
rs12060032	0.83[ASN][1000 genomes]
rs12562113	0.88[ASN][1000 genomes]
rs12566278	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12568734	0.97[ASN][1000 genomes]
rs1258055	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1258058	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258063	0.86[ASN][1000 genomes]
rs1258064	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258065	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258066	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258068	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1258072	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1268714	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1273237	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13374909	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1745376	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1933932	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2146560	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2181412	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2241863	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241864	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439442	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2476153	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2476155	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2476156	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2476157	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2476159	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2486160	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2486162	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3011290	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3766218	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766220	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766221	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766222	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56771521	0.97[ASN][1000 genomes]
rs57495753	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs582269	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs582323	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs582760	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs583649	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58920789	0.83[ASN][1000 genomes]
rs59479990	0.97[ASN][1000 genomes]
rs596794	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs597221	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60239027	0.83[ASN][1000 genomes]
rs604233	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs604264	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs611919	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs629412	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs631368	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs631840	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs636082	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs636122	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs636424	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs648822	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs654544	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs655369	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs657166	0.96[ASN][1000 genomes]
rs669647	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs673134	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs675731	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs678466	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs683585	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs685862	0.85[AMR][1000 genomes]
rs689300	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs723333	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs724309	0.90[EUR][1000 genomes]
rs72896683	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72900715	0.97[ASN][1000 genomes]
rs736188	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9094	0.80[AMR][1000 genomes];0.89[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	chr1:47134600-47157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:47138000-47157800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr1:47138200-47159400	Strong transcription	Placenta	Placenta
4	chr1:47138400-47158800	Strong transcription	Fetal Muscle Trunk	muscle
5	chr1:47138400-47159400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:47138800-47158600	Strong transcription	Primary B cells from cord blood	blood
7	chr1:47139000-47159400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:47139200-47159400	Strong transcription	Brain Germinal Matrix	brain
9	chr1:47139200-47159800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:47139400-47159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:47139600-47159400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:47140000-47155400	Strong transcription	HSMM	muscle
13	chr1:47141200-47157800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:47141400-47183400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:47142000-47159400	Strong transcription	K562	blood
16	chr1:47142000-47159800	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr1:47142400-47158000	Strong transcription	HMEC	breast
18	chr1:47142600-47158200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:47142600-47159200	Strong transcription	GM12878-XiMat	blood
20	chr1:47142600-47159400	Strong transcription	NHEK	skin
21	chr1:47142800-47158800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:47142800-47159600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr1:47142800-47159800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:47143200-47153600	Strong transcription	Brain Angular Gyrus	brain
25	chr1:47143200-47159400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:47143200-47159400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:47143200-47159800	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:47143600-47158400	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:47143600-47159400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:47143800-47158200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:47143800-47159400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:47143800-47159400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:47143800-47159800	Strong transcription	Primary T cells from cord blood	blood
34	chr1:47143800-47171600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr1:47144000-47158200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:47144600-47159600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:47145000-47158000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:47145400-47158000	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr1:47145400-47159000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:47145600-47157800	Strong transcription	NH-A	brain
41	chr1:47145800-47155800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr1:47145800-47158800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:47147000-47158200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
44	chr1:47147600-47158400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:47147800-47155800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:47147800-47157200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:47148000-47158000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:47148000-47158200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:47148000-47158200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:47148200-47153600	Strong transcription	Brain Cingulate Gyrus	brain

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