Variant report

Variant	rs1258066
Chromosome Location	chr1:47103172-47103173
allele	A/G
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	chr1:47101531..47103755-chr1:47107864..47109587,2	K562	blood:
3	chr1:47096461..47099303-chr1:47102647..47105072,2	K562	blood:
4	chr1:47093097..47096139-chr1:47100393..47103970,3	K562	blood:
5	chr1:47089433..47091250-chr1:47102705..47105351,2	K562	blood:
6	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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10890414	0.85[ASN][1000 genomes]
rs11211332	1.00[EUR][1000 genomes]
rs11211343	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11801744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12568734	0.85[ASN][1000 genomes]
rs1258055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1258058	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258063	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1258064	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]
rs1258065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258068	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258072	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1268714	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1273237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13374909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1745376	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1933932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146560	0.84[AMR][1000 genomes];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];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2241864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2439442	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2476153	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2476155	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2476156	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2476157	0.96[AFR][1000 genomes];0.92[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];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2486162	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3011290	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3766218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766223	1.00[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];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs582323	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs582760	0.96[AFR][1000 genomes];0.92[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];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs597221	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs604233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs604264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs611919	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs629412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs631368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs631840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs636082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs636122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs654544	0.96[AFR][1000 genomes];0.92[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];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6677350	1.00[CEU][hapmap]
rs669647	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs673134	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs675731	0.98[AFR][1000 genomes];1.00[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	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs685862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs689300	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs723333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724309	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[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];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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	chr1:47094200-47103400	Strong transcription	Fetal Muscle Leg	muscle
11	chr1:47094200-47105800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:47094400-47103800	Strong transcription	Primary T cells from cord blood	blood
13	chr1:47094600-47105600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr1:47094600-47111000	Strong transcription	Fetal Muscle Trunk	muscle
15	chr1:47094600-47119200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:47095200-47107800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:47095400-47103600	Strong transcription	Liver	Liver
18	chr1:47095600-47103200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:47095600-47104000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:47095600-47109000	Strong transcription	Placenta	Placenta
21	chr1:47095800-47104600	Weak transcription	A549	lung
22	chr1:47096000-47103400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:47096400-47103200	Strong transcription	Fetal Brain Female	brain
24	chr1:47096600-47103800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:47096600-47105800	Strong transcription	Brain Anterior Caudate	brain
26	chr1:47096800-47103600	Strong transcription	Brain Hippocampus Middle	brain
27	chr1:47096800-47103800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:47096800-47105600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:47097000-47103600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:47097000-47103600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:47097000-47104000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:47097000-47104000	Strong transcription	Fetal Lung	lung
33	chr1:47097000-47104000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:47097000-47105800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr1:47097200-47103400	Strong transcription	Primary B cells from cord blood	blood
36	chr1:47097200-47103600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:47097200-47103600	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr1:47097200-47103800	Strong transcription	Thymus	Thymus
39	chr1:47097200-47106000	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr1:47097600-47103200	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:47098000-47103200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:47098200-47109000	Weak transcription	Esophagus	oesophagus
43	chr1:47098200-47113200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr1:47098400-47112800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:47099600-47104000	Strong transcription	Fetal Stomach	stomach
46	chr1:47099800-47103600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr1:47099800-47104000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:47099800-47106000	Weak transcription	K562	blood
49	chr1:47100000-47113400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:47100200-47103200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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