Variant report

Variant	rs649950
Chromosome Location	chr4:1090786-1090787
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:1086221..1088731-chr4:1090765..1092594,2	MCF-7	breast:
2	chr4:1073585..1077671-chr4:1089546..1092795,3	MCF-7	breast:
3	chr4:1090535..1093016-chr4:1094804..1097177,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178222	Chromatin interaction
ENSG00000251639	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10032349	0.88[AFR][1000 genomes]
rs10032470	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11724989	1.00[YRI][hapmap]
rs11732520	0.93[YRI][hapmap]
rs13119696	0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs13146371	0.81[AFR][1000 genomes]
rs1383660	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1466214	0.93[YRI][hapmap]
rs1680027	0.91[AFR][1000 genomes]
rs17729286	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1825092	0.82[AFR][1000 genomes]
rs28510738	0.92[AFR][1000 genomes]
rs28514301	0.92[AFR][1000 genomes]
rs28588234	0.92[AFR][1000 genomes]
rs2924495	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4246683	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4246684	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4974561	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4974569	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4974571	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4974573	0.94[YRI][hapmap]
rs4974628	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4974637	0.81[AMR][1000 genomes]
rs4974639	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4974642	0.93[YRI][hapmap];0.81[AMR][1000 genomes]
rs4974643	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4974644	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs55741287	0.81[AFR][1000 genomes]
rs583100	0.91[AFR][1000 genomes]
rs584472	0.84[AFR][1000 genomes]
rs588824	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs589660	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs59057706	0.92[AFR][1000 genomes]
rs604526	0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs606293	0.91[AFR][1000 genomes]
rs606327	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs608066	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs614945	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs615381	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs616196	0.92[AFR][1000 genomes]
rs616569	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs619407	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs620398	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs629638	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs630549	0.92[AFR][1000 genomes]
rs632319	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs633087	0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs633141	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs633599	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs633954	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs636976	0.94[AFR][1000 genomes]
rs643043	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs646117	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs647828	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs648640	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs649243	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs649258	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs649616	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs651135	0.92[AFR][1000 genomes]
rs651509	0.92[AFR][1000 genomes]
rs658320	0.92[AFR][1000 genomes]
rs661364	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs674347	0.91[AFR][1000 genomes]
rs6814094	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs681857	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs682243	0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs682787	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6839768	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6840162	0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6840347	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs687939	0.92[AFR][1000 genomes]
rs689216	0.92[AFR][1000 genomes]
rs73074169	0.92[AFR][1000 genomes]
rs7686839	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7691553	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	esv3355565	chr4:1087452-1092050	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	esv3493482	chr4:1087652-1091450	Enhancers Bivalent Enhancer Genic enhancers Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	esv3493483	chr4:1088265-1090926	Weak transcription Bivalent Enhancer Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	esv3493481	chr4:1088702-1091300	Weak transcription Bivalent Enhancer Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	esv3493484	chr4:1088702-1091300	Weak transcription Bivalent Enhancer Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs649950	AC092574.2	cis	lung	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1084200-1093400	Weak transcription	Ovary	ovary
2	chr4:1086000-1098400	Weak transcription	Lung	lung
3	chr4:1086200-1091400	Weak transcription	Gastric	stomach
4	chr4:1086200-1098600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:1088400-1093400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:1088600-1093600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:1090400-1093400	Enhancers	Pancreas	Pancrea
8	chr4:1090600-1091000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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