Variant report

Variant	rs56156703
Chromosome Location	chr3:160258869-160258870
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160257431..160260761-chr3:160280958..160284866,4	MCF-7	breast:
2	chr3:160164299..160166121-chr3:160258126..160260628,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186432	Chromatin interaction
ENSG00000229320	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1047210	0.84[EUR][1000 genomes]
rs11706810	0.84[EUR][1000 genomes]
rs11718121	0.83[EUR][1000 genomes]
rs12632030	0.82[EUR][1000 genomes]
rs1369666	0.90[EUR][1000 genomes]
rs1451760	0.83[EUR][1000 genomes]
rs1551190	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1584688	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17236473	0.85[EUR][1000 genomes]
rs17826221	0.84[EUR][1000 genomes]
rs1971128	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2123003	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2886825	0.82[ASN][1000 genomes]
rs3732706	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3773372	0.83[AMR][1000 genomes]
rs3851365	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4679654	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4679888	0.82[AMR][1000 genomes]
rs4679890	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4679891	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4679895	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4680589	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4680591	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55992947	0.82[EUR][1000 genomes]
rs56197102	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62272791	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62272792	0.84[AMR][1000 genomes]
rs62272794	0.84[AMR][1000 genomes]
rs6785881	0.84[EUR][1000 genomes]
rs6809153	0.80[EUR][1000 genomes]
rs7355951	0.80[EUR][1000 genomes]
rs7618974	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7621724	0.82[ASN][1000 genomes]
rs7640072	0.84[AMR][1000 genomes]
rs7643779	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7647873	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	nsv877701	chr3:160228001-160283815	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56156703	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160217400-160259600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:160219800-160263600	Weak transcription	Right Ventricle	heart
3	chr3:160220600-160261200	Weak transcription	Pancreas	Pancrea
4	chr3:160225600-160259800	Weak transcription	Stomach Mucosa	stomach
5	chr3:160234600-160261000	Weak transcription	Spleen	Spleen
6	chr3:160234600-160281000	Weak transcription	Aorta	Aorta
7	chr3:160235000-160266600	Weak transcription	Esophagus	oesophagus
8	chr3:160239600-160265200	Weak transcription	Brain Substantia Nigra	brain
9	chr3:160240200-160280400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:160244200-160272200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:160244400-160263400	Weak transcription	Small Intestine	intestine
12	chr3:160244800-160259600	Weak transcription	Brain Angular Gyrus	brain
13	chr3:160245000-160259800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:160245200-160262200	Weak transcription	Fetal Kidney	kidney
15	chr3:160246600-160279200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:160246800-160266400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:160247000-160259800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:160247000-160261000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:160247000-160270400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:160247000-160281000	Weak transcription	Thymus	Thymus
21	chr3:160248400-160261200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:160248400-160261200	Weak transcription	Gastric	stomach
23	chr3:160248400-160261200	Weak transcription	Lung	lung
24	chr3:160248400-160261200	Weak transcription	Ovary	ovary
25	chr3:160248400-160261600	Weak transcription	Fetal Stomach	stomach
26	chr3:160248800-160263000	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:160248800-160268600	Weak transcription	NHLF	lung
28	chr3:160249200-160261200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:160249200-160279000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:160249800-160261600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:160250400-160271600	Weak transcription	HepG2	liver
32	chr3:160250600-160259400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:160251000-160266800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:160251200-160261000	Weak transcription	Left Ventricle	heart
35	chr3:160251200-160282000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:160251600-160263400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:160251800-160263000	Weak transcription	GM12878-XiMat	blood
38	chr3:160252200-160260000	Weak transcription	A549	lung
39	chr3:160252400-160267200	Weak transcription	Primary B cells from cord blood	blood
40	chr3:160252800-160259000	Weak transcription	Fetal Thymus	thymus
41	chr3:160252800-160261200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:160252800-160272600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:160253000-160263400	Weak transcription	Fetal Muscle Leg	muscle
44	chr3:160253000-160264800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:160253000-160267400	Weak transcription	Fetal Intestine Small	intestine
46	chr3:160253000-160272000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr3:160253200-160265200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:160253400-160259600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:160253400-160262200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:160253400-160265200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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