Variant report

Variant	rs62088870
Chromosome Location	chr18:9594326-9594327
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:9593651..9596050-chr18:9613258..9616024,2	MCF-7	breast:
2	chr18:9593285..9595195-chr18:9598496..9600998,2	K562	blood:

Variant related genes	Relation type
ENSG00000154845	Chromatin interaction
ENSG00000263627	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1036930	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11081487	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12327541	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16955297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869737	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1869738	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1869739	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2028657	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840354	0.93[ASN][1000 genomes]
rs3786174	0.83[ASN][1000 genomes]
rs55841197	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56883068	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57539299	0.93[ASN][1000 genomes]
rs58800301	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58982927	0.93[ASN][1000 genomes]
rs59114729	0.83[ASN][1000 genomes]
rs59992205	0.83[ASN][1000 genomes]
rs60290408	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61166388	0.83[ASN][1000 genomes]
rs61275183	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62086146	0.83[ASN][1000 genomes]
rs62086147	0.83[ASN][1000 genomes]
rs62086151	0.83[ASN][1000 genomes]
rs62086152	0.83[ASN][1000 genomes]
rs62086155	0.83[ASN][1000 genomes]
rs62086156	0.83[ASN][1000 genomes]
rs62086158	0.83[ASN][1000 genomes]
rs62086159	0.83[ASN][1000 genomes]
rs62087363	0.83[ASN][1000 genomes]
rs62087368	0.83[ASN][1000 genomes]
rs62087370	0.83[ASN][1000 genomes]
rs62087371	0.83[ASN][1000 genomes]
rs62087378	0.83[ASN][1000 genomes]
rs62087402	0.83[ASN][1000 genomes]
rs62087403	0.83[ASN][1000 genomes]
rs62087404	0.83[ASN][1000 genomes]
rs62087406	0.83[ASN][1000 genomes]
rs62087407	0.83[ASN][1000 genomes]
rs62087411	0.83[ASN][1000 genomes]
rs62087412	0.83[ASN][1000 genomes]
rs62087414	0.83[ASN][1000 genomes]
rs62087415	0.83[ASN][1000 genomes]
rs62087416	0.83[ASN][1000 genomes]
rs62087417	0.80[ASN][1000 genomes]
rs62087427	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62087456	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088860	0.97[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088872	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088873	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088875	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088876	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62088880	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088881	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088884	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088885	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088904	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088906	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62088908	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6506677	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7228280	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7231531	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7233308	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7233649	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7234355	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7235935	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7236274	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7237018	0.93[ASN][1000 genomes]
rs7238137	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7239083	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72945737	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs732698	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73393880	0.83[ASN][1000 genomes]
rs73395717	0.83[ASN][1000 genomes]
rs73395719	0.83[ASN][1000 genomes]
rs8096551	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs894757	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv543644	chr18:9576145-9612516	Strong transcription Enhancers Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9545800-9595200	Strong transcription	Dnd41	blood
2	chr18:9551000-9612200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr18:9553800-9613600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr18:9563600-9594800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr18:9566800-9594600	Strong transcription	HSMM	muscle
6	chr18:9570400-9594400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr18:9576000-9594400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr18:9576200-9597800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr18:9577600-9594400	Weak transcription	Stomach Mucosa	stomach
10	chr18:9578400-9595200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr18:9578800-9594800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr18:9581000-9595400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr18:9581400-9595800	Weak transcription	Brain Angular Gyrus	brain
14	chr18:9581400-9609200	Weak transcription	Pancreas	Pancrea
15	chr18:9582000-9594600	Weak transcription	Psoas Muscle	Psoas
16	chr18:9582000-9597000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr18:9582400-9594600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr18:9582800-9594400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr18:9582800-9594600	Weak transcription	Fetal Heart	heart
20	chr18:9582800-9597600	Weak transcription	Fetal Brain Male	brain
21	chr18:9583400-9595000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr18:9583600-9595000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr18:9584800-9596600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr18:9585000-9597200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr18:9586400-9594400	Strong transcription	HepG2	liver
26	chr18:9586600-9594400	Strong transcription	NHEK	skin
27	chr18:9586600-9595200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr18:9586800-9594400	Strong transcription	Osteobl	bone
29	chr18:9588200-9594600	Weak transcription	Gastric	stomach
30	chr18:9588200-9594600	Weak transcription	Small Intestine	intestine
31	chr18:9588200-9595800	Weak transcription	Spleen	Spleen
32	chr18:9588600-9595000	Weak transcription	Right Ventricle	heart
33	chr18:9588600-9612400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr18:9588800-9594400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr18:9588800-9594600	Weak transcription	Brain Anterior Caudate	brain
36	chr18:9588800-9594600	Weak transcription	Fetal Lung	lung
37	chr18:9588800-9595000	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr18:9588800-9595800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr18:9589000-9594400	Weak transcription	Colon Smooth Muscle	Colon
40	chr18:9589000-9594600	Weak transcription	Brain Hippocampus Middle	brain
41	chr18:9589000-9594600	Weak transcription	Brain Substantia Nigra	brain
42	chr18:9589000-9594600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr18:9589000-9594600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr18:9589000-9594600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr18:9589000-9594600	Weak transcription	HSMMtube	muscle
46	chr18:9589000-9594800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr18:9589000-9595000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr18:9589000-9595000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr18:9589000-9595000	Weak transcription	A549	lung
50	chr18:9589000-9595200	Weak transcription	Primary T cells fromperipheralblood	blood

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