Variant report

Variant	rs488345
Chromosome Location	chr1:93558036-93558037
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93551802..93553578-chr1:93556864..93558399,2	K562	blood:
2	chr1:93551871..93559721-chr1:93563340..93568184,9	K562	blood:
3	chr1:93543191..93547486-chr1:93556671..93562707,7	K562	blood:
4	chr1:93543139..93547854-chr1:93556364..93561572,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143033	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1064797	0.97[EUR][1000 genomes]
rs12080248	1.00[ASN][1000 genomes]
rs12404947	0.94[EUR][1000 genomes]
rs12405666	0.91[EUR][1000 genomes]
rs12409621	0.91[EUR][1000 genomes]
rs12736775	1.00[ASN][1000 genomes]
rs17131703	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17131705	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.98[EUR][1000 genomes]
rs17131709	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17131710	1.00[CEU][hapmap];0.91[GIH][hapmap];0.94[EUR][1000 genomes]
rs17386609	0.91[EUR][1000 genomes]
rs2749734	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2785602	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2785605	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815419	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2815423	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2815424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41286823	0.97[EUR][1000 genomes]
rs41292137	0.94[EUR][1000 genomes]
rs4240965	0.87[EUR][1000 genomes]
rs4347219	0.91[EUR][1000 genomes]
rs475120	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.98[EUR][1000 genomes]
rs490153	1.00[ASN][1000 genomes]
rs495580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500349	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502651	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs519319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs539544	1.00[ASW][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546445	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs548751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550892	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs566843	1.00[ASN][1000 genomes]
rs571439	0.98[EUR][1000 genomes]
rs574687	0.98[EUR][1000 genomes]
rs57992499	0.97[EUR][1000 genomes]
rs580828	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60458375	0.94[EUR][1000 genomes]
rs61433067	0.97[EUR][1000 genomes]
rs6604041	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6604042	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66501175	0.94[EUR][1000 genomes]
rs6670960	1.00[ASN][1000 genomes]
rs6689007	0.97[EUR][1000 genomes]
rs6696026	1.00[ASN][1000 genomes]
rs67002303	0.94[EUR][1000 genomes]
rs6702666	0.89[ASN][1000 genomes]
rs6703169	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.98[MKK][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67262037	0.97[EUR][1000 genomes]
rs67337461	0.94[EUR][1000 genomes]
rs67395827	0.94[EUR][1000 genomes]
rs67711178	0.97[EUR][1000 genomes]
rs67723709	0.94[EUR][1000 genomes]
rs67768103	0.94[EUR][1000 genomes]
rs67992203	0.97[EUR][1000 genomes]
rs72715364	0.94[EUR][1000 genomes]
rs72715394	0.91[EUR][1000 genomes]
rs72717318	0.89[EUR][1000 genomes]
rs72717334	0.94[EUR][1000 genomes]
rs72717337	0.91[EUR][1000 genomes]
rs72717346	0.92[EUR][1000 genomes]
rs72717352	0.94[EUR][1000 genomes]
rs72717354	0.91[EUR][1000 genomes]
rs72717374	0.91[EUR][1000 genomes]
rs72719120	0.94[EUR][1000 genomes]
rs72955366	0.97[EUR][1000 genomes]
rs72955388	0.97[EUR][1000 genomes]
rs72959223	0.94[EUR][1000 genomes]
rs72959288	0.94[EUR][1000 genomes]
rs72959296	0.91[EUR][1000 genomes]
rs7555395	1.00[ASN][1000 genomes]
rs797594	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[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	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

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93545800-93563200	Weak transcription	Esophagus	oesophagus
2	chr1:93545800-93568000	Weak transcription	Gastric	stomach
3	chr1:93545800-93578400	Weak transcription	Pancreas	Pancrea
4	chr1:93546000-93560600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:93546000-93573000	Weak transcription	Placenta	Placenta
6	chr1:93546200-93563200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:93546200-93602200	Weak transcription	Aorta	Aorta
8	chr1:93546400-93563200	Weak transcription	Psoas Muscle	Psoas
9	chr1:93546400-93567200	Weak transcription	Right Atrium	heart
10	chr1:93546400-93569400	Weak transcription	Ovary	ovary
11	chr1:93546600-93559000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:93547200-93559000	Weak transcription	Brain Hippocampus Middle	brain
13	chr1:93547200-93576800	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:93547400-93581800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:93547600-93559400	Weak transcription	Brain Angular Gyrus	brain
16	chr1:93547600-93559400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:93547600-93560200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:93547600-93580600	Weak transcription	Adipose Nuclei	Adipose
19	chr1:93547600-93580600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:93547600-93600000	Weak transcription	HSMMtube	muscle
21	chr1:93547800-93575400	Weak transcription	Hela-S3	cervix
22	chr1:93547800-93580600	Weak transcription	Fetal Kidney	kidney
23	chr1:93548000-93559000	Weak transcription	NHDF-Ad	bronchial
24	chr1:93548000-93601800	Weak transcription	NHLF	lung
25	chr1:93548200-93558200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:93548200-93576600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:93548200-93576600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:93548200-93576800	Weak transcription	Osteobl	bone
29	chr1:93548200-93578400	Weak transcription	Lung	lung
30	chr1:93548600-93569400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:93548800-93559000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:93548800-93559600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:93548800-93581600	Weak transcription	Small Intestine	intestine
34	chr1:93549000-93576800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:93549000-93582400	Weak transcription	HMEC	breast
36	chr1:93549000-93582800	Weak transcription	NHEK	skin
37	chr1:93550000-93559400	Weak transcription	Brain Substantia Nigra	brain
38	chr1:93550600-93572600	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:93551400-93558600	Weak transcription	HepG2	liver
40	chr1:93551400-93563400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:93551400-93579800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr1:93551600-93558400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:93551600-93559000	Weak transcription	Thymus	Thymus
44	chr1:93551600-93559200	Weak transcription	Liver	Liver
45	chr1:93551600-93559800	Weak transcription	Brain Anterior Caudate	brain
46	chr1:93551600-93570800	Weak transcription	HUVEC	blood vessel
47	chr1:93551600-93571000	Weak transcription	Fetal Intestine Large	intestine
48	chr1:93551600-93573000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:93551600-93578400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:93551800-93558600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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