Variant report

Variant	rs2858084
Chromosome Location	chr4:3272118-3272119
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3243269..3245646-chr4:3270348..3272217,2	MCF-7	breast:
2	chr4:3269730..3272201-chr4:3294200..3296416,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10805008	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10937921	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2071667	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071668	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2071671	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2108753	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2157090	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2157091	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2157092	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2530597	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2530599	0.87[ASN][1000 genomes]
rs2530601	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2798221	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2798222	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2798224	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2798225	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2858083	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2858085	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2858086	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2858087	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2858088	0.91[ASN][1000 genomes]
rs3095072	0.83[ASN][1000 genomes]
rs3095073	0.83[ASN][1000 genomes]
rs3095074	0.80[ASN][1000 genomes]
rs3095077	0.93[ASN][1000 genomes]
rs3095079	0.94[ASN][1000 genomes]
rs3095080	0.88[ASN][1000 genomes]
rs3095081	0.83[ASN][1000 genomes]
rs3095082	0.83[ASN][1000 genomes]
rs3095083	0.83[ASN][1000 genomes]
rs3121420	0.91[ASN][1000 genomes]
rs3129319	0.94[ASN][1000 genomes]
rs3129320	0.91[ASN][1000 genomes]
rs3135064	0.86[ASN][1000 genomes]
rs3135168	0.89[ASN][1000 genomes]
rs3135169	0.81[ASN][1000 genomes]
rs3135170	0.80[ASN][1000 genomes]
rs3135171	0.80[ASN][1000 genomes]
rs362279	0.80[ASN][1000 genomes]
rs362283	0.81[ASN][1000 genomes]
rs6446726	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6446727	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6446728	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6446731	0.80[ASN][1000 genomes]
rs7656026	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7661630	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7674472	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7675084	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9996868	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	63 gene(s)	inside rSNPs	diseases
3	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv470003	chr4:3215835-3275484	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv878454	chr4:3215835-3305739	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
7	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv878457	chr4:3231661-3278517	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv878458	chr4:3235518-3303976	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv878459	chr4:3235518-3310831	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
12	nsv878460	chr4:3260154-3303976	Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
13	nsv878461	chr4:3270488-3339038	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription 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 target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3260200-3278200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr4:3264200-3273000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:3269200-3272400	Enhancers	Fetal Brain Male	brain
4	chr4:3269400-3272400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr4:3269400-3272600	Enhancers	Fetal Brain Female	brain
6	chr4:3269400-3273200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:3269600-3272400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr4:3269600-3272800	Enhancers	Fetal Muscle Leg	muscle
9	chr4:3269800-3272400	Enhancers	Brain Germinal Matrix	brain
10	chr4:3270000-3274400	Weak transcription	Gastric	stomach
11	chr4:3270800-3272400	Enhancers	Fetal Heart	heart
12	chr4:3270800-3272800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr4:3271000-3272400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr4:3271000-3272400	Enhancers	Brain Hippocampus Middle	brain
15	chr4:3271000-3272400	Enhancers	Left Ventricle	heart
16	chr4:3271200-3272600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr4:3271400-3272200	Bivalent Enhancer	Fetal Stomach	stomach
18	chr4:3271400-3272400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr4:3271400-3272400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr4:3271600-3272200	Enhancers	Right Ventricle	heart
21	chr4:3271800-3272200	Enhancers	Brain Cingulate Gyrus	brain
22	chr4:3271800-3272200	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr4:3271800-3272200	Flanking Active TSS	HSMM	muscle
24	chr4:3271800-3272400	Enhancers	HSMMtube	muscle
25	chr4:3272000-3272200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr4:3272000-3272400	Enhancers	Pancreas	Pancrea
27	chr4:3272000-3272400	Enhancers	Psoas Muscle	Psoas
28	chr4:3272000-3272400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr4:3272000-3272400	Flanking Bivalent TSS/Enh	HepG2	liver

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