Variant report

Variant	rs56258146
Chromosome Location	chr3:50488333-50488334
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	chr3:50486710..50489241-chr3:50648575..50650420,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114738	Chromatin interaction
ENSG00000114737	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1034408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1034409	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11914549	0.81[AFR][1000 genomes]
rs2157328	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2187815	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2236969	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2236972	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2236976	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2236977	1.00[EUR][1000 genomes]
rs2236978	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2236982	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2236990	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2282757	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28428559	1.00[EUR][1000 genomes]
rs28580410	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28593422	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41305886	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4422301	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55790255	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55876418	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55892059	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56114301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56249615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56287038	0.81[AFR][1000 genomes]
rs56766970	1.00[EUR][1000 genomes]
rs57405128	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57415469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58412961	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59012751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59790001	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60149721	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60273100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60391761	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60697422	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61413553	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61493458	1.00[EUR][1000 genomes]
rs6767505	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6770258	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6770669	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73832879	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73832881	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833363	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833366	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833372	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73833373	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73833386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835503	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73835505	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs743754	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs743755	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7610830	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7612820	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7617345	0.81[AFR][1000 genomes]
rs7625295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7626470	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7634307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7640842	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7642779	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7647409	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649603	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9311451	1.00[EUR][1000 genomes]
rs9311453	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9814606	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9817768	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828829	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9832993	0.82[EUR][1000 genomes]
rs9837658	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9837861	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9843693	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9854585	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9863307	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9883635	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9990256	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
4	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
5	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS 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 miRNA target site	104 gene(s)	inside rSNPs	diseases
7	nsv834693	chr3:50302830-50507964	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription 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 miRNA target site	87 gene(s)	inside rSNPs	diseases
8	nsv876775	chr3:50324672-50504896	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
9	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
12	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	esv3445182	chr3:50458687-50496660	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription 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
15	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers 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

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50482200-50493400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:50483800-50488600	Enhancers	Lung	lung
3	chr3:50484000-50500800	Weak transcription	Pancreas	Pancrea
4	chr3:50486400-50488400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr3:50486600-50488400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:50486600-50488400	Enhancers	Spleen	Spleen
7	chr3:50486600-50488600	Enhancers	Primary hematopoietic stem cells	blood
8	chr3:50486600-50488600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:50486800-50488400	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:50486800-50488400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:50486800-50488800	Enhancers	Fetal Thymus	thymus
12	chr3:50487000-50488400	Enhancers	H1 Cell Line	embryonic stem cell
13	chr3:50487000-50488400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:50487000-50488400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:50487000-50488400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:50487000-50488600	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr3:50487000-50488600	Active TSS	Stomach Smooth Muscle	stomach
18	chr3:50487000-50489200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:50487200-50488400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr3:50487200-50488600	Enhancers	Fetal Intestine Large	intestine
21	chr3:50487200-50488600	Enhancers	Stomach Mucosa	stomach
22	chr3:50487400-50488400	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr3:50487400-50488400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:50487400-50488400	Enhancers	Fetal Muscle Trunk	muscle
25	chr3:50487400-50488400	Flanking Active TSS	HepG2	liver
26	chr3:50487400-50488600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:50487400-50488600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:50487400-50488600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr3:50487400-50488600	Enhancers	Brain Angular Gyrus	brain
30	chr3:50487400-50488600	Bivalent Enhancer	Fetal Brain Male	brain
31	chr3:50487400-50488600	Enhancers	Fetal Muscle Leg	muscle
32	chr3:50487600-50493600	Weak transcription	Colonic Mucosa	Colon
33	chr3:50487600-50493800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:50487800-50488400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr3:50487800-50488400	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr3:50487800-50488400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:50487800-50488400	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr3:50487800-50488400	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr3:50487800-50488400	Flanking Active TSS	Fetal Intestine Small	intestine
40	chr3:50487800-50488400	Active TSS	Rectal Smooth Muscle	rectum
41	chr3:50487800-50488400	Flanking Active TSS	Osteobl	bone
42	chr3:50487800-50488600	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr3:50488000-50488400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:50488000-50488400	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr3:50488000-50488400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr3:50488000-50488400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr3:50488000-50488400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr3:50488000-50488400	Active TSS	Brain Cingulate Gyrus	brain
49	chr3:50488000-50488400	Enhancers	Brain Hippocampus Middle	brain
50	chr3:50488000-50488400	Active TSS	Colon Smooth Muscle	Colon

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