Variant report

Variant	rs1258064
Chromosome Location	chr1:47103891-47103892
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47101531..47106665-chr1:47107497..47111745,7	K562	blood:
2	chr1:47096461..47099303-chr1:47102647..47105072,2	K562	blood:
3	chr1:47093097..47096139-chr1:47100393..47103970,3	K562	blood:
4	chr1:47089433..47091250-chr1:47102705..47105351,2	K562	blood:
5	chr1:47102903..47105171-chr1:47109988..47112496,2	K562	blood:

Variant related genes	Relation type
ENSG00000123472	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10890410	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10890414	0.85[ASN][1000 genomes]
rs11211332	1.00[EUR][1000 genomes]
rs11211343	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11801744	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12059860	1.00[CEU][hapmap]
rs12562113	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12566278	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12568734	0.85[ASN][1000 genomes]
rs1258055	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1258058	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258063	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1258065	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258066	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258068	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258072	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1268714	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1273237	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13374909	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1745376	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1933932	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146560	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181412	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241863	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2241864	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2439442	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2476153	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2476155	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2476156	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2476157	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2476159	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2486160	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2486162	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3011290	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3766218	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766221	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3766222	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766223	0.95[CHB][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56771521	0.85[ASN][1000 genomes]
rs57495753	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs582269	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs582323	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs582760	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs583649	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58678760	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59479990	0.85[ASN][1000 genomes]
rs596794	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs597221	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs604233	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs604264	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs611919	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs629412	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs631368	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs631840	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs636082	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs636122	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs636424	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs648822	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs654544	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs655369	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs657166	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6677350	1.00[CEU][hapmap]
rs669647	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs673134	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs675731	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs678466	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs683585	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs685862	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs689300	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs723333	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724309	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72896683	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72900715	0.85[ASN][1000 genomes]
rs736188	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9094	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.88[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	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
4	nsv945926	chr1:47100728-47104475	Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	1 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	chr1:47083200-47104600	Weak transcription	Stomach Mucosa	stomach
2	chr1:47083200-47115000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:47083400-47113200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:47088200-47131600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:47088600-47108600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:47088600-47108800	Weak transcription	Hela-S3	cervix
7	chr1:47089800-47112400	Weak transcription	Small Intestine	intestine
8	chr1:47090200-47121400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:47091400-47105000	Weak transcription	HMEC	breast
10	chr1:47094200-47105800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:47094600-47105600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:47094600-47111000	Strong transcription	Fetal Muscle Trunk	muscle
13	chr1:47094600-47119200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:47095200-47107800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:47095600-47104000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:47095600-47109000	Strong transcription	Placenta	Placenta
17	chr1:47095800-47104600	Weak transcription	A549	lung
18	chr1:47096600-47105800	Strong transcription	Brain Anterior Caudate	brain
19	chr1:47096800-47105600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr1:47097000-47104000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:47097000-47104000	Strong transcription	Fetal Lung	lung
22	chr1:47097000-47104000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:47097000-47105800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr1:47097200-47106000	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr1:47098200-47109000	Weak transcription	Esophagus	oesophagus
26	chr1:47098200-47113200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:47098400-47112800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:47099600-47104000	Strong transcription	Fetal Stomach	stomach
29	chr1:47099800-47104000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:47099800-47106000	Weak transcription	K562	blood
31	chr1:47100000-47113400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:47100200-47104000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:47100200-47107200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:47100800-47104000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:47101200-47109400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:47101600-47104800	Weak transcription	Fetal Kidney	kidney
37	chr1:47101600-47104800	Weak transcription	HepG2	liver
38	chr1:47101600-47105000	Weak transcription	NHEK	skin
39	chr1:47101600-47108800	Weak transcription	GM12878-XiMat	blood
40	chr1:47101600-47130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:47101600-47133000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr1:47101800-47105000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:47101800-47105000	Weak transcription	NHLF	lung
44	chr1:47101800-47107000	Weak transcription	Fetal Thymus	thymus
45	chr1:47101800-47107600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:47101800-47107800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:47101800-47108000	Weak transcription	NH-A	brain
48	chr1:47101800-47108600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:47101800-47108800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:47101800-47109000	Weak transcription	Pancreas	Pancrea

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