Variant report

Variant	rs62293577
Chromosome Location	chr4:1169273-1169274
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	chr4:1161114..1165211-chr4:1166165..1170804,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C4orf42-5	chr4:1168591-1170378	NONHSAT094675

Variant related genes	Relation type
ENSG00000273179	Chromatin interaction
ENSG00000159674	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10014526	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10020143	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11538062	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11937228	0.89[ASN][1000 genomes]
rs28478922	0.82[ASN][1000 genomes]
rs28660089	0.89[ASN][1000 genomes]
rs28750743	0.89[ASN][1000 genomes]
rs28883944	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28886387	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3755953	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60044123	0.89[ASN][1000 genomes]
rs73792281	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1009619	chr4:901897-1215657	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv1003876	chr4:927509-1191316	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1000381	chr4:927509-1198766	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
7	nsv1012892	chr4:1086871-1176630	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
9	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
10	nsv878329	chr4:1147407-1254930	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
11	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
12	nsv519106	chr4:1158991-1174861	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv593276	chr4:1159680-1227469	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv461151	chr4:1159680-1236840	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv593277	chr4:1159680-1236840	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	nsv878331	chr4:1159680-1254930	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
17	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
18	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62293577	KIAA1530	Cis_1M	lymphoblastoid	RTeQTL
rs62293577	CRIPAK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1166600-1169600	Enhancers	Psoas Muscle	Psoas
2	chr4:1166600-1170800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:1166600-1171000	Weak transcription	Gastric	stomach
4	chr4:1167000-1169800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr4:1167000-1174200	Weak transcription	Primary T cells from cord blood	blood
6	chr4:1167200-1169600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:1167200-1170000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:1167200-1170800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr4:1167200-1172800	Weak transcription	Right Atrium	heart
10	chr4:1167200-1174200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:1167400-1170200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:1167400-1171200	Weak transcription	Brain Anterior Caudate	brain
13	chr4:1167400-1172600	Weak transcription	Lung	lung
14	chr4:1167400-1173400	Enhancers	Fetal Muscle Leg	muscle
15	chr4:1167600-1170200	Weak transcription	Fetal Kidney	kidney
16	chr4:1167600-1170600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr4:1167800-1170600	Weak transcription	Left Ventricle	heart
18	chr4:1167800-1170800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr4:1167800-1170800	Weak transcription	Esophagus	oesophagus
20	chr4:1167800-1170800	Weak transcription	HSMMtube	muscle
21	chr4:1167800-1171200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:1167800-1171200	Weak transcription	Osteobl	bone
23	chr4:1167800-1173800	Enhancers	Liver	Liver
24	chr4:1168000-1170800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:1168000-1170800	Weak transcription	Right Ventricle	heart
26	chr4:1168000-1170800	Enhancers	HepG2	liver
27	chr4:1168000-1171000	Weak transcription	NHDF-Ad	bronchial
28	chr4:1168000-1171000	Weak transcription	NHLF	lung
29	chr4:1168000-1172200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:1168200-1170400	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr4:1168400-1170000	Bivalent Enhancer	Fetal Stomach	stomach
32	chr4:1168600-1169800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:1168800-1169600	Enhancers	Stomach Smooth Muscle	stomach
34	chr4:1169000-1169400	Enhancers	Pancreas	Pancrea
35	chr4:1169000-1170000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr4:1169000-1170600	Weak transcription	Spleen	Spleen
37	chr4:1169000-1171000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr4:1169200-1169600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:1169200-1170800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:1169200-1171000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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