Variant report

Variant	rs12566278
Chromosome Location	chr1:47112195-47112196
allele	C/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	GATA3	chr1:47111849-47112596	SK-N-SH	brain:	n/a	chr1:47112095-47112102 chr1:47112097-47112106 chr1:47112099-47112106 chr1:47112096-47112108
2	GATA3	chr1:47111866-47112567	SK-N-SH	brain:	n/a	chr1:47112095-47112102 chr1:47112097-47112106 chr1:47112099-47112106 chr1:47112096-47112108

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47080354..47082092-chr1:47110886..47112430,2	MCF-7	breast:

Variant related genes	Relation type
ATPAF1	TF binding region
ENSG00000142961	Chromatin interaction

Extended variants
information (count: 79 )
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	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11211332	0.89[EUR][1000 genomes]
rs11211343	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11801744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12059860	1.00[CEU][hapmap]
rs12562113	0.85[ASN][1000 genomes]
rs12568734	0.87[ASN][1000 genomes]
rs1258055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1258058	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258063	0.95[ASN][1000 genomes]
rs1258064	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258068	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1258072	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1268714	0.98[ASN][1000 genomes]
rs1273237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13374909	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];0.98[ASN][1000 genomes]
rs1745376	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1933932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2146560	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2181412	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2241864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2439442	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2476153	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476155	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2476156	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476157	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2476159	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2486160	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2486162	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011290	0.86[ASN][1000 genomes]
rs3766218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766221	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3766222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3766223	1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56771521	0.87[ASN][1000 genomes]
rs57495753	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs582269	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs582323	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs582760	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs583649	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58678760	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59479990	0.87[ASN][1000 genomes]
rs596794	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs597221	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs604233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs604264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs611919	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs629412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs631368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs631840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs636082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs636122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636424	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs648822	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs654544	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs655369	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs657166	0.92[ASN][1000 genomes]
rs6677350	1.00[CEU][hapmap]
rs669647	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs673134	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs675731	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs678466	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs683585	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs685862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs689300	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs723333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724309	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs72896683	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72900715	0.87[ASN][1000 genomes]
rs736188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[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	chr1:47083200-47115000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:47083400-47113200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:47088200-47131600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:47089800-47112400	Weak transcription	Small Intestine	intestine
5	chr1:47090200-47121400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:47094600-47119200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:47098200-47113200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:47098400-47112800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:47100000-47113400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:47101600-47130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:47101600-47133000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:47101800-47112400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:47101800-47112600	Weak transcription	Lung	lung
14	chr1:47101800-47112800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:47101800-47113000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:47101800-47115000	Weak transcription	Dnd41	blood
17	chr1:47101800-47115200	Weak transcription	Gastric	stomach
18	chr1:47101800-47119000	Weak transcription	Colonic Mucosa	Colon
19	chr1:47101800-47121200	Weak transcription	HUVEC	blood vessel
20	chr1:47102000-47115000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:47102000-47122400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:47102400-47121400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:47103000-47112800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:47103000-47115200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:47103000-47115200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:47103000-47132800	Weak transcription	Spleen	Spleen
27	chr1:47103200-47113200	Weak transcription	Fetal Brain Female	brain
28	chr1:47105000-47132800	Weak transcription	Stomach Mucosa	stomach
29	chr1:47105600-47113800	Weak transcription	Fetal Intestine Small	intestine
30	chr1:47105800-47112600	Weak transcription	NHEK	skin
31	chr1:47105800-47115200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:47106800-47114600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:47107000-47113800	Weak transcription	Fetal Stomach	stomach
34	chr1:47107000-47115200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:47107400-47113600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:47107600-47112800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:47107800-47115200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:47108200-47112200	Weak transcription	Liver	Liver
39	chr1:47108200-47112800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:47108200-47113200	Enhancers	Colon Smooth Muscle	Colon
41	chr1:47108200-47123400	Weak transcription	K562	blood
42	chr1:47108400-47112400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:47108800-47115200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:47109000-47112600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:47109000-47113000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:47109000-47115400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:47109200-47112200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:47109200-47112600	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:47109200-47112600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:47109200-47112600	Weak transcription	Right Ventricle	heart

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