Variant report

Variant	rs12632030
Chromosome Location	chr3:160133339-160133340
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:160132801-160133959	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:160132741-160133872	K562	blood:	n/a	n/a
3	POLR2A	chr3:160133238-160133900	U87	brain:	n/a	n/a
4	MAFF	chr3:160133214-160133542	K562	blood:	n/a	n/a
5	POLR2A	chr3:160132869-160133891	A549	lung:	n/a	n/a
6	POLR2A	chr3:160133303-160133423	Hela-S3	cervix:	n/a	n/a
7	MAFK	chr3:160133327-160133573	K562	blood:	n/a	n/a
8	MAFK	chr3:160133286-160133539	IMR90	lung:	n/a	n/a
9	POLR2A	chr3:160133282-160133834	U87	brain:	n/a	n/a
10	MAFK	chr3:160133259-160133519	HepG2	liver:	n/a	n/a
11	SPI1	chr3:160133202-160133633	HL-60	blood:	n/a	n/a
12	CEBPB	chr3:160133166-160133386	K562	blood:	n/a	n/a
13	MAFK	chr3:160133218-160133536	HepG2	liver:	n/a	n/a
14	MAFF	chr3:160133221-160133518	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:160127070-160138790	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160117087..160119597-chr3:160131636..160133939,3	MCF-7	breast:
2	chr3:160131935..160134663-chr3:160164828..160167325,4	K562	blood:
3	chr3:160131739..160133430-chr3:160134002..160136220,2	MCF-7	breast:
4	chr3:160116969..160117938-chr3:160133064..160134013,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
SMC4	TF binding region
ENSG00000213186	Chromatin interaction
ENSG00000068885	Chromatin interaction
ENSG00000113810	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1047210	0.87[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10923	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10936201	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10936203	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs11706810	0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11708118	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11709232	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs11709336	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11718121	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11719750	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11720689	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12639488	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1369666	0.81[EUR][1000 genomes]
rs1451760	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236473	0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17236494	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs17826221	0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17826257	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs1873076	0.82[CHB][hapmap];1.00[JPT][hapmap]
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]
rs55992947	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56156703	0.82[EUR][1000 genomes]
rs6785881	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6790951	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6791056	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6798183	0.86[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6809153	0.86[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7355951	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7620828	0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7627555	0.86[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs869467	0.96[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
rs12632030	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160119000-160144600	Weak transcription	Spleen	Spleen
2	chr3:160119000-160145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:160119400-160137800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:160119400-160144400	Weak transcription	Pancreas	Pancrea
5	chr3:160119400-160144600	Weak transcription	Gastric	stomach
6	chr3:160119600-160133800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:160119800-160142000	Weak transcription	Psoas Muscle	Psoas
8	chr3:160119800-160144400	Weak transcription	Esophagus	oesophagus
9	chr3:160119800-160144600	Weak transcription	Lung	lung
10	chr3:160119800-160144600	Weak transcription	Ovary	ovary
11	chr3:160119800-160144600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:160119800-160145200	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:160119800-160146600	Weak transcription	HSMMtube	muscle
14	chr3:160119800-160151800	Weak transcription	Brain Substantia Nigra	brain
15	chr3:160120200-160152400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:160120200-160164400	Weak transcription	Fetal Brain Male	brain
17	chr3:160120400-160134800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:160120800-160133400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:160121200-160144400	Weak transcription	Colonic Mucosa	Colon
20	chr3:160121200-160157200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:160121200-160157400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:160121200-160157800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:160121800-160134000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:160122000-160139800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:160122000-160144800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr3:160122000-160161000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:160122000-160164400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:160122000-160164600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:160122200-160157400	Strong transcription	Fetal Thymus	thymus
30	chr3:160122400-160134200	Weak transcription	Fetal Brain Female	brain
31	chr3:160122400-160135000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:160122600-160155000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:160122600-160156600	Strong transcription	K562	blood
34	chr3:160122800-160154200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:160123000-160153600	Weak transcription	Brain Anterior Caudate	brain
36	chr3:160123200-160133400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:160123200-160155400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:160124000-160159000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr3:160124200-160152600	Strong transcription	Hela-S3	cervix
40	chr3:160124600-160155000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:160125000-160144400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:160125200-160159800	Strong transcription	HSMM	muscle
43	chr3:160125800-160133400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:160126800-160137600	Weak transcription	Fetal Heart	heart
45	chr3:160127800-160154000	Strong transcription	HMEC	breast
46	chr3:160127800-160157000	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr3:160128000-160154200	Strong transcription	Dnd41	blood
48	chr3:160128200-160152400	Strong transcription	GM12878-XiMat	blood
49	chr3:160128400-160157200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:160128600-160158200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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