Variant report

Variant	rs475120
Chromosome Location	chr1:93573253-93573254
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1064797	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12062154	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12404947	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12405666	0.92[EUR][1000 genomes]
rs12409621	0.92[EUR][1000 genomes]
rs17131703	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];1.00[ASN][1000 genomes]
rs17131705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17131709	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17131710	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17386609	0.92[EUR][1000 genomes]
rs2391228	1.00[ASN][1000 genomes]
rs2749734	0.97[EUR][1000 genomes]
rs2783489	0.86[YRI][hapmap]
rs2785602	0.97[EUR][1000 genomes]
rs2785605	0.97[EUR][1000 genomes]
rs2815419	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2815423	0.97[EUR][1000 genomes]
rs2815424	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs41286823	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41292137	0.95[EUR][1000 genomes]
rs4240964	0.87[AFR][1000 genomes]
rs4240965	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4347219	0.92[EUR][1000 genomes]
rs488345	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.98[EUR][1000 genomes]
rs495580	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs500349	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs502651	0.87[EUR][1000 genomes]
rs519319	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs539544	1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs548751	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs550892	1.00[CHD][hapmap]
rs571439	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574687	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57992499	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs580828	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs60458375	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61433067	0.98[EUR][1000 genomes]
rs6604042	0.97[EUR][1000 genomes]
rs66501175	0.95[EUR][1000 genomes]
rs6689007	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67002303	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6703169	1.00[CEU][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs67262037	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67337461	0.95[EUR][1000 genomes]
rs67395827	0.95[EUR][1000 genomes]
rs67711178	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67723709	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67768103	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67992203	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72715364	0.95[EUR][1000 genomes]
rs72715394	0.92[EUR][1000 genomes]
rs72717318	0.91[EUR][1000 genomes]
rs72717334	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72717337	0.92[EUR][1000 genomes]
rs72717346	0.94[EUR][1000 genomes]
rs72717352	0.95[EUR][1000 genomes]
rs72717354	0.92[EUR][1000 genomes]
rs72717374	0.92[EUR][1000 genomes]
rs72719120	0.95[EUR][1000 genomes]
rs72955366	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72955388	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72959223	0.95[EUR][1000 genomes]
rs72959288	0.95[EUR][1000 genomes]
rs72959296	0.92[EUR][1000 genomes]
rs797594	0.88[EUR][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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv508404	chr1:93547383-93580012	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh 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:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93545800-93578400	Weak transcription	Pancreas	Pancrea
2	chr1:93546200-93602200	Weak transcription	Aorta	Aorta
3	chr1:93547200-93576800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr1:93547400-93581800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:93547600-93580600	Weak transcription	Adipose Nuclei	Adipose
6	chr1:93547600-93580600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:93547600-93600000	Weak transcription	HSMMtube	muscle
8	chr1:93547800-93575400	Weak transcription	Hela-S3	cervix
9	chr1:93547800-93580600	Weak transcription	Fetal Kidney	kidney
10	chr1:93548000-93601800	Weak transcription	NHLF	lung
11	chr1:93548200-93576600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:93548200-93576600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:93548200-93576800	Weak transcription	Osteobl	bone
14	chr1:93548200-93578400	Weak transcription	Lung	lung
15	chr1:93548800-93581600	Weak transcription	Small Intestine	intestine
16	chr1:93549000-93576800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:93549000-93582400	Weak transcription	HMEC	breast
18	chr1:93549000-93582800	Weak transcription	NHEK	skin
19	chr1:93551400-93579800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:93551600-93578400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:93551800-93576600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:93551800-93579800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:93552000-93580000	Weak transcription	NH-A	brain
24	chr1:93552200-93573600	Weak transcription	Fetal Lung	lung
25	chr1:93555400-93581000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:93559400-93576600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:93559400-93581000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:93560000-93573800	Weak transcription	Liver	Liver
29	chr1:93560200-93575600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:93560200-93581600	Weak transcription	Brain Anterior Caudate	brain
31	chr1:93560400-93574400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:93561800-93575400	Weak transcription	HepG2	liver
33	chr1:93563400-93582000	Weak transcription	Esophagus	oesophagus
34	chr1:93564000-93581800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:93564200-93574400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:93565000-93574000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
38	chr1:93566600-93575400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:93566600-93575600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr1:93566600-93576800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:93567400-93574000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:93567400-93575400	Weak transcription	Left Ventricle	heart
43	chr1:93567800-93573800	Strong transcription	Dnd41	blood
44	chr1:93567800-93575400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr1:93568400-93584200	Weak transcription	Fetal Brain Male	brain
46	chr1:93569200-93573400	Strong transcription	K562	blood
47	chr1:93569200-93574600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:93569200-93574800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:93569400-93574600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:93569400-93574600	ZNF genes & repeats	GM12878-XiMat	blood

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