Variant report

Variant	rs6791056
Chromosome Location	chr3:160025238-160025239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160024329..160027233-chr3:160115797..160118305,2	K562	blood:
2	chr3:159942931..159944766-chr3:160024081..160025820,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244040	Chromatin interaction
ENSG00000068885	Chromatin interaction
ENSG00000113810	Chromatin interaction
ENSG00000244078	Chromatin interaction
ENSG00000180044	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1047210	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11706810	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11718121	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12632030	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1451760	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17236473	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17826221	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3851365	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55992947	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6785881	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6790951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798183	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6809153	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7355951	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7620828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7627555	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs869467	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6791056	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159971400-160035800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:159974200-160038000	Weak transcription	Fetal Brain Male	brain
3	chr3:159975000-160025600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:159975000-160028000	Weak transcription	Brain Anterior Caudate	brain
5	chr3:159975000-160034200	Weak transcription	Fetal Intestine Large	intestine
6	chr3:159975200-160036000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:159975600-160046600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:159976200-160039000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:159977800-160073000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:159981200-160038200	Weak transcription	Esophagus	oesophagus
11	chr3:159984800-160038200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:159988200-160030200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:159992400-160035400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:159992800-160026400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:159992800-160033400	Weak transcription	Fetal Kidney	kidney
16	chr3:159992800-160036400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr3:159992800-160036600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:159995400-160034200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:159996400-160037000	Weak transcription	Primary B cells from cord blood	blood
20	chr3:159996600-160038400	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:159996800-160033600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:159997000-160033800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:159997200-160037200	Weak transcription	Brain Angular Gyrus	brain
24	chr3:159997200-160046600	Weak transcription	Fetal Lung	lung
25	chr3:159997600-160035600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:159999600-160027000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:159999800-160033800	Weak transcription	Aorta	Aorta
28	chr3:159999800-160034000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:159999800-160035400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:159999800-160047800	Weak transcription	Lung	lung
31	chr3:160010000-160033000	Weak transcription	Fetal Intestine Small	intestine
32	chr3:160010000-160034000	Weak transcription	Pancreas	Pancrea
33	chr3:160010000-160047800	Weak transcription	HepG2	liver
34	chr3:160010000-160048600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:160010000-160048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:160010200-160034000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr3:160010800-160032000	Weak transcription	Fetal Muscle Leg	muscle
38	chr3:160012200-160033000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:160013400-160028800	Weak transcription	Fetal Stomach	stomach
40	chr3:160014600-160039400	Weak transcription	GM12878-XiMat	blood
41	chr3:160014800-160037200	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:160014800-160039600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:160015000-160027800	Weak transcription	NHLF	lung
44	chr3:160015000-160038200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:160015000-160044000	Weak transcription	Osteobl	bone
46	chr3:160015200-160027200	Weak transcription	Adipose Nuclei	Adipose
47	chr3:160015400-160048400	Weak transcription	A549	lung
48	chr3:160015800-160026600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:160015800-160048800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:160016400-160025600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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