Variant report

Variant	rs3731495
Chromosome Location	chr3:48227337-48227338
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48226160..48232247-chr3:48279704..48285684,8	K562	blood:
2	chr3:48218514..48223617-chr3:48225606..48230757,7	MCF-7	breast:
3	chr3:48221961..48224816-chr3:48225047..48228042,2	MCF-7	breast:
4	chr3:47422216..47424027-chr3:48225306..48227849,2	K562	blood:

Variant related genes	Relation type
ENSG00000164048	Chromatin interaction
ENSG00000253056	Chromatin interaction
ENSG00000260236	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000231884	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10780032	1.00[EUR][1000 genomes]
rs11130169	1.00[EUR][1000 genomes]
rs3731539	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3731547	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4476528	1.00[AMR][1000 genomes]
rs4858818	1.00[EUR][1000 genomes]
rs55808934	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442092	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442103	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6442104	1.00[AMR][1000 genomes]
rs6773945	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6793732	1.00[EUR][1000 genomes]
rs6801348	1.00[EUR][1000 genomes]
rs7372108	1.00[AMR][1000 genomes]
rs73831540	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831544	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831562	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831565	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831572	1.00[EUR][1000 genomes]
rs7633433	1.00[EUR][1000 genomes]
rs9852211	1.00[EUR][1000 genomes]
rs9863220	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9917799	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv1012024	chr3:48119229-48242670	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS 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	33 gene(s)	inside rSNPs	diseases
8	nsv834682	chr3:48138137-48311122	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48193000-48228400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:48193600-48228200	Weak transcription	Pancreas	Pancrea
3	chr3:48193800-48228400	Weak transcription	Adipose Nuclei	Adipose
4	chr3:48193800-48228600	Weak transcription	Brain Substantia Nigra	brain
5	chr3:48193800-48228800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:48194000-48228400	Weak transcription	Right Ventricle	heart
7	chr3:48194000-48228800	Weak transcription	Left Ventricle	heart
8	chr3:48197800-48227600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:48198400-48227600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:48198400-48227800	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr3:48198400-48228000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:48198400-48228000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:48198400-48228200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:48198400-48228200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:48199000-48227600	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:48199200-48227800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:48199800-48228000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:48200000-48227600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr3:48200200-48227800	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr3:48203400-48228200	Weak transcription	Colonic Mucosa	Colon
21	chr3:48204400-48228400	Weak transcription	Fetal Brain Male	brain
22	chr3:48205000-48227600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:48205200-48228400	Weak transcription	Primary B cells from cord blood	blood
24	chr3:48205400-48227600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:48206000-48228400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:48206000-48228400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:48206200-48228600	Weak transcription	Brain Anterior Caudate	brain
28	chr3:48207200-48228400	Weak transcription	Placenta	Placenta
29	chr3:48207200-48228400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:48207400-48228600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr3:48208400-48228200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:48209400-48228600	Weak transcription	Primary T cells from cord blood	blood
33	chr3:48212200-48227400	Weak transcription	Stomach Mucosa	stomach
34	chr3:48212200-48227800	Strong transcription	Fetal Thymus	thymus
35	chr3:48213400-48227400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:48213600-48227600	Strong transcription	A549	lung
37	chr3:48213600-48227800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:48214200-48228400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:48214400-48228400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:48215200-48227800	Strong transcription	HSMM	muscle
41	chr3:48215800-48228400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:48216000-48228200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:48217600-48228200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:48217800-48228400	Weak transcription	Spleen	Spleen
45	chr3:48219400-48228400	Weak transcription	Esophagus	oesophagus
46	chr3:48220800-48227600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:48221000-48227400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:48221400-48228000	Weak transcription	Fetal Brain Female	brain
49	chr3:48222000-48227400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:48223600-48227400	Strong transcription	ES-I3 Cell Line	embryonic stem cell

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