Variant report

Variant	rs6852246
Chromosome Location	chr4:1052556-1052557
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:1052002..1052766-chr4:1359397..1360108,2	MCF-7	breast:
2	chr4:1045118..1048090-chr4:1052343..1053975,2	K562	blood:

Variant related genes	Relation type
ENSG00000163945	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10032349	0.82[EUR][1000 genomes]
rs10032470	0.82[EUR][1000 genomes]
rs10033163	0.82[EUR][1000 genomes]
rs11724989	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11731238	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11732259	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1383660	0.82[EUR][1000 genomes]
rs1680027	0.95[EUR][1000 genomes]
rs28374671	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28510738	0.95[EUR][1000 genomes]
rs28514301	0.95[EUR][1000 genomes]
rs28579427	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28588234	0.95[EUR][1000 genomes]
rs2924495	0.85[EUR][1000 genomes]
rs4974561	0.82[EUR][1000 genomes]
rs4974628	0.82[EUR][1000 genomes]
rs4974637	0.82[EUR][1000 genomes]
rs4974639	0.82[EUR][1000 genomes]
rs4974642	0.82[EUR][1000 genomes]
rs4974643	0.82[EUR][1000 genomes]
rs4974644	0.82[EUR][1000 genomes]
rs56308648	0.86[EUR][1000 genomes]
rs583100	0.95[EUR][1000 genomes]
rs584472	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs588824	0.82[EUR][1000 genomes]
rs589660	0.85[EUR][1000 genomes]
rs59057706	0.93[EUR][1000 genomes]
rs60085185	0.88[EUR][1000 genomes]
rs604526	0.95[EUR][1000 genomes]
rs606293	0.95[EUR][1000 genomes]
rs606327	0.95[EUR][1000 genomes]
rs608066	0.95[EUR][1000 genomes]
rs614945	0.95[EUR][1000 genomes]
rs615381	0.95[EUR][1000 genomes]
rs616196	0.95[EUR][1000 genomes]
rs616569	0.85[EUR][1000 genomes]
rs617633	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs619407	0.85[EUR][1000 genomes]
rs620398	0.85[EUR][1000 genomes]
rs629638	0.95[EUR][1000 genomes]
rs630549	0.95[EUR][1000 genomes]
rs632319	0.85[EUR][1000 genomes]
rs633087	0.85[EUR][1000 genomes]
rs633141	0.85[EUR][1000 genomes]
rs633599	0.85[EUR][1000 genomes]
rs633954	0.95[EUR][1000 genomes]
rs636976	0.93[EUR][1000 genomes]
rs643043	0.95[EUR][1000 genomes]
rs646117	0.85[EUR][1000 genomes]
rs647828	0.85[EUR][1000 genomes]
rs648640	0.85[EUR][1000 genomes]
rs649243	0.95[EUR][1000 genomes]
rs649258	0.85[EUR][1000 genomes]
rs649616	0.85[EUR][1000 genomes]
rs651135	0.95[EUR][1000 genomes]
rs651509	0.95[EUR][1000 genomes]
rs658320	0.95[EUR][1000 genomes]
rs661364	0.85[EUR][1000 genomes]
rs671790	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs674347	0.93[EUR][1000 genomes]
rs6814094	0.85[EUR][1000 genomes]
rs6814276	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6817989	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs681857	0.85[EUR][1000 genomes]
rs682243	0.85[EUR][1000 genomes]
rs682787	0.85[EUR][1000 genomes]
rs6840162	0.82[EUR][1000 genomes]
rs687939	0.95[EUR][1000 genomes]
rs689216	0.95[EUR][1000 genomes]
rs73072227	0.88[EUR][1000 genomes]
rs73074169	0.95[EUR][1000 genomes]
rs7682141	0.88[EUR][1000 genomes]
rs9992322	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 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	nsv878258	chr4:712222-1058358	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1003219	chr4:769894-1105464	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv432547	chr4:782301-1053930	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv878266	chr4:793929-1058358	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv469998	chr4:809593-1087531	Strong transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv878272	chr4:809787-1058358	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv878277	chr4:813393-1087531	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv1012895	chr4:827866-1054874	Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv536979	chr4:827866-1054874	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv536980	chr4:827866-1167377	Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	nsv870410	chr4:927839-1090974	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
17	nsv878291	chr4:939883-1058358	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
18	nsv878292	chr4:939883-1087531	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
19	nsv878295	chr4:941518-1064116	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
20	esv1846290	chr4:941518-1081307	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
21	esv1799097	chr4:944191-1053162	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
22	nsv878304	chr4:946974-1058358	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
23	nsv878312	chr4:965779-1058358	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
24	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
25	nsv878314	chr4:976918-1058358	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
26	esv1842515	chr4:983060-1087531	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
27	nsv878325	chr4:1011115-1058358	Weak transcription Bivalent Enhancer Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
28	nsv1004727	chr4:1015652-1158207	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
29	nsv536984	chr4:1015652-1158207	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
30	nsv1005990	chr4:1015652-1167619	Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
31	nsv878327	chr4:1024752-1087531	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
32	nsv1000594	chr4:1045099-1129975	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
33	nsv1001165	chr4:1051512-1129975	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
34	esv1815338	chr4:1052100-1063187	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6852246	AC092574.2	cis	lung	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1049600-1054600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:1049800-1056200	Weak transcription	Right Atrium	heart
3	chr4:1050000-1052800	Weak transcription	Spleen	Spleen
4	chr4:1050000-1054600	Weak transcription	Pancreas	Pancrea
5	chr4:1050000-1055400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:1050200-1054200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:1050400-1055600	Weak transcription	GM12878-XiMat	blood
8	chr4:1051000-1052800	Bivalent Enhancer	Stomach Mucosa	stomach
9	chr4:1051800-1053400	Enhancers	Fetal Heart	heart
10	chr4:1052000-1052600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:1052000-1053000	Enhancers	Right Ventricle	heart
12	chr4:1052000-1053600	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr4:1052200-1052600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:1052200-1052800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:1052200-1052800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:1052200-1052800	Enhancers	Esophagus	oesophagus
17	chr4:1052200-1053000	Enhancers	Gastric	stomach
18	chr4:1052200-1053400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr4:1052400-1052800	Enhancers	Left Ventricle	heart
20	chr4:1052400-1053000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:1052400-1053000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:1052400-1053000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr4:1052400-1053000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
24	chr4:1052400-1053000	Bivalent Enhancer	HMEC	breast
25	chr4:1052400-1053200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:1052400-1053400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
27	chr4:1052400-1053400	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum

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