Variant report

Variant	rs878324
Chromosome Location	chr4:1169851-1169852
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:1161675..1163555-chr4:1169840..1172430,2	MCF-7	breast:
2	chr4:1161114..1165211-chr4:1166165..1170804,4	MCF-7	breast:
3	chr4:1161599..1163141-chr4:1169473..1171016,2	K562	blood:

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

Variant related genes	Relation type
ENSG00000159674	Chromatin interaction
ENSG00000273179	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10002248	1.00[ASN][1000 genomes]
rs10002437	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10003030	0.87[AFR][1000 genomes]
rs10014245	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10015944	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10016588	0.85[AFR][1000 genomes]
rs10027895	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10029139	1.00[ASN][1000 genomes]
rs11247974	1.00[ASN][1000 genomes]
rs11726554	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11731643	0.86[AFR][1000 genomes]
rs11731685	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11732057	1.00[ASN][1000 genomes]
rs11734374	1.00[ASN][1000 genomes]
rs13435166	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1481167	0.85[AFR][1000 genomes]
rs17164384	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28540372	0.90[AFR][1000 genomes]
rs28578449	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28621675	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs28785628	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28855974	1.00[ASN][1000 genomes]
rs28856334	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3775111	0.91[AFR][1000 genomes]
rs59465697	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6599282	0.85[AFR][1000 genomes]
rs6599283	0.85[AFR][1000 genomes]
rs6599284	1.00[ASN][1000 genomes]
rs6599285	1.00[ASN][1000 genomes]
rs6812059	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6831018	0.84[AFR][1000 genomes]
rs6836158	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6836335	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73065688	0.84[AMR][1000 genomes]
rs73065696	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73065698	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73067706	1.00[ASN][1000 genomes]
rs73067775	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73067776	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73219741	1.00[ASN][1000 genomes]
rs7669287	0.91[AFR][1000 genomes]
rs7676956	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7678661	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7679718	1.00[ASN][1000 genomes]
rs7684536	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7685051	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7690300	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7690832	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[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

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1166600-1170800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr4:1166600-1171000	Weak transcription	Gastric	stomach
3	chr4:1167000-1174200	Weak transcription	Primary T cells from cord blood	blood
4	chr4:1167200-1170000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:1167200-1170800	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr4:1167200-1172800	Weak transcription	Right Atrium	heart
7	chr4:1167200-1174200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:1167400-1170200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:1167400-1171200	Weak transcription	Brain Anterior Caudate	brain
10	chr4:1167400-1172600	Weak transcription	Lung	lung
11	chr4:1167400-1173400	Enhancers	Fetal Muscle Leg	muscle
12	chr4:1167600-1170200	Weak transcription	Fetal Kidney	kidney
13	chr4:1167600-1170600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:1167800-1170600	Weak transcription	Left Ventricle	heart
15	chr4:1167800-1170800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:1167800-1170800	Weak transcription	Esophagus	oesophagus
17	chr4:1167800-1170800	Weak transcription	HSMMtube	muscle
18	chr4:1167800-1171200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:1167800-1171200	Weak transcription	Osteobl	bone
20	chr4:1167800-1173800	Enhancers	Liver	Liver
21	chr4:1168000-1170800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:1168000-1170800	Weak transcription	Right Ventricle	heart
23	chr4:1168000-1170800	Enhancers	HepG2	liver
24	chr4:1168000-1171000	Weak transcription	NHDF-Ad	bronchial
25	chr4:1168000-1171000	Weak transcription	NHLF	lung
26	chr4:1168000-1172200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr4:1168200-1170400	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr4:1168400-1170000	Bivalent Enhancer	Fetal Stomach	stomach
29	chr4:1169000-1170000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
30	chr4:1169000-1170600	Weak transcription	Spleen	Spleen
31	chr4:1169000-1171000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr4:1169200-1170800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:1169200-1171000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:1169400-1170800	Weak transcription	Pancreas	Pancrea
35	chr4:1169600-1170600	Weak transcription	Psoas Muscle	Psoas
36	chr4:1169600-1170800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:1169600-1170800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr4:1169800-1170800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:1169800-1170800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr4:1169800-1173200	Enhancers	Primary T cells fromperipheralblood	blood
41	chr4:1169800-1173200	Enhancers	Fetal Muscle Trunk	muscle

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