Variant report

Variant	rs55992947
Chromosome Location	chr3:160123373-160123374
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160121669..160124122-chr3:160164375..160167615,4	MCF-7	breast:
2	chr3:160116116..160127665-chr3:160158037..160169627,42	K562	blood:
3	chr3:160116116..160124648-chr3:160162504..160168767,20	K562	blood:

Variant related genes	Relation type
ENSG00000213186	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1047210	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11706810	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11718121	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12632030	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1369666	0.81[EUR][1000 genomes]
rs1451760	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236473	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17826221	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1971128	0.84[EUR][1000 genomes]
rs3732706	0.81[EUR][1000 genomes]
rs3851365	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4679654	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4680589	0.83[EUR][1000 genomes]
rs4680591	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56156703	0.82[EUR][1000 genomes]
rs6785881	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6790951	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6791056	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6798183	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6809153	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7355951	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7620828	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7627555	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs869467	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
7	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
8	esv1795255	chr3:160089896-160153305	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	205 gene(s)	inside rSNPs	diseases
9	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55992947	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160118000-160123400	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr3:160119000-160144600	Weak transcription	Spleen	Spleen
3	chr3:160119000-160145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:160119400-160128000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:160119400-160129000	Weak transcription	Brain Angular Gyrus	brain
6	chr3:160119400-160130400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:160119400-160130400	Weak transcription	Left Ventricle	heart
8	chr3:160119400-160137800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:160119400-160144400	Weak transcription	Pancreas	Pancrea
10	chr3:160119400-160144600	Weak transcription	Gastric	stomach
11	chr3:160119600-160133800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:160119800-160126000	Weak transcription	Stomach Mucosa	stomach
13	chr3:160119800-160130000	Weak transcription	Placenta	Placenta
14	chr3:160119800-160130400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:160119800-160130400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:160119800-160130400	Weak transcription	Small Intestine	intestine
17	chr3:160119800-160130600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:160119800-160132400	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:160119800-160132400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:160119800-160142000	Weak transcription	Psoas Muscle	Psoas
21	chr3:160119800-160144400	Weak transcription	Esophagus	oesophagus
22	chr3:160119800-160144600	Weak transcription	Lung	lung
23	chr3:160119800-160144600	Weak transcription	Ovary	ovary
24	chr3:160119800-160144600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:160119800-160145200	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:160119800-160146600	Weak transcription	HSMMtube	muscle
27	chr3:160119800-160151800	Weak transcription	Brain Substantia Nigra	brain
28	chr3:160120000-160123800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:160120000-160132400	Weak transcription	Right Ventricle	heart
30	chr3:160120200-160132200	Weak transcription	Adipose Nuclei	Adipose
31	chr3:160120200-160152400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:160120200-160164400	Weak transcription	Fetal Brain Male	brain
33	chr3:160120400-160134800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:160120600-160130200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:160120600-160130400	Weak transcription	Fetal Intestine Small	intestine
36	chr3:160120600-160132400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:160120800-160124600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:160120800-160130600	Weak transcription	Fetal Intestine Large	intestine
39	chr3:160120800-160133400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr3:160121000-160123400	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr3:160121000-160127600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:160121000-160129800	Weak transcription	Liver	Liver
43	chr3:160121000-160130400	Weak transcription	Fetal Stomach	stomach
44	chr3:160121000-160131800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:160121000-160132000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:160121200-160127600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:160121200-160130400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr3:160121200-160132400	Weak transcription	Fetal Kidney	kidney
49	chr3:160121200-160144400	Weak transcription	Colonic Mucosa	Colon
50	chr3:160121200-160157200	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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