Variant report

Variant	rs2476159
Chromosome Location	chr1:47124884-47124885
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:47124121..47126688-chr1:47131484..47133286,2	K562	blood:
2	chr1:47124455..47128063-chr1:47131072..47135010,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123472	Chromatin interaction
ENSG00000186118	Chromatin interaction
ENSG00000233647	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10890410	0.94[ASN][1000 genomes]
rs10890414	0.91[ASN][1000 genomes]
rs11211332	1.00[EUR][1000 genomes]
rs11211343	0.91[ASN][1000 genomes]
rs11801744	0.91[ASN][1000 genomes]
rs12562113	0.90[ASN][1000 genomes]
rs12566278	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12568734	0.91[ASN][1000 genomes]
rs1258055	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1258058	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1258063	0.88[ASN][1000 genomes]
rs1258064	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1258065	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1258066	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1258068	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1258072	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1268714	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1273237	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13374909	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1745376	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1933932	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2146560	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2181412	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241863	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241864	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2439442	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2476153	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2476155	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2476156	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2476157	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2486160	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2486162	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3011290	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3766218	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766220	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766221	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3766222	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766223	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56771521	0.91[ASN][1000 genomes]
rs57495753	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs582269	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs582323	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs582760	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs583649	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58678760	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59479990	0.91[ASN][1000 genomes]
rs596794	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs597221	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs604233	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs604264	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs611919	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs629412	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs631368	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs631840	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs636082	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs636122	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs636424	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs648822	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs654544	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs655369	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs657166	0.98[ASN][1000 genomes]
rs669647	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs673134	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs675731	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs678466	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs683585	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs685862	0.85[AMR][1000 genomes]
rs689300	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs723333	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs724309	0.90[EUR][1000 genomes]
rs72896683	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72900715	0.91[ASN][1000 genomes]
rs736188	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9094	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47088200-47131600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:47101600-47130000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:47101600-47133000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:47103000-47132800	Weak transcription	Spleen	Spleen
5	chr1:47105000-47132800	Weak transcription	Stomach Mucosa	stomach
6	chr1:47109400-47129800	Weak transcription	Pancreas	Pancrea
7	chr1:47109400-47132600	Weak transcription	Hela-S3	cervix
8	chr1:47109600-47132600	Weak transcription	HMEC	breast
9	chr1:47112200-47125600	Strong transcription	Liver	Liver
10	chr1:47112400-47126800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr1:47112800-47125400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:47112800-47125800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:47115000-47125200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr1:47115000-47125400	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:47115600-47133000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:47115800-47132000	Weak transcription	Fetal Heart	heart
17	chr1:47116000-47127400	Weak transcription	Fetal Stomach	stomach
18	chr1:47116000-47130000	Weak transcription	Lung	lung
19	chr1:47116000-47130600	Weak transcription	Esophagus	oesophagus
20	chr1:47116000-47131800	Weak transcription	Aorta	Aorta
21	chr1:47116600-47130000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:47116600-47131400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:47117000-47125200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:47117600-47125200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:47117600-47125400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr1:47117600-47125400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:47117600-47125600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:47117600-47125600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr1:47117600-47125600	Strong transcription	Placenta	Placenta
30	chr1:47117600-47125800	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr1:47117600-47127200	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:47117600-47127600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:47117600-47127600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:47117800-47126000	Strong transcription	Fetal Muscle Leg	muscle
35	chr1:47117800-47126400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:47118000-47125400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr1:47118000-47125600	Strong transcription	Primary hematopoietic stem cells	blood
38	chr1:47118000-47125600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:47118000-47126600	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr1:47118000-47126600	Strong transcription	Brain Anterior Caudate	brain
41	chr1:47118000-47132800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:47118200-47130000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr1:47119000-47132400	Weak transcription	A549	lung
44	chr1:47119200-47125200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:47119200-47132400	Weak transcription	Small Intestine	intestine
46	chr1:47119400-47126000	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:47119600-47125000	Weak transcription	Fetal Brain Male	brain
48	chr1:47119800-47126200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:47120000-47126400	Strong transcription	Duodenum Mucosa	Duodenum
50	chr1:47120000-47127400	Weak transcription	Fetal Intestine Small	intestine

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