Variant report

Variant	rs12630564
Chromosome Location	chr3:160170243-160170244
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:122)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:160170070-160170253	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:160170169-160170273	A549	lung:	n/a	n/a
3	ELF1	chr3:160170069-160170324	K562	blood:	n/a	chr3:160170228-160170241 chr3:160170178-160170187
4	MYC	chr3:160170113-160170306	MCF-7	breast:	n/a	n/a
5	HEY1	chr3:160170121-160170367	K562	blood:	n/a	n/a
6	POLR2A	chr3:160170167-160170421	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:160170033-160170267	A549	lung:	n/a	n/a
8	POLR2A	chr3:160169983-160170265	H1-hESC	embryonic stem cell:	n/a	n/a
9	USF1	chr3:160170178-160170371	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:160170136-160170303	H1-hESC	embryonic stem cell:	n/a	n/a
11	ELF1	chr3:160170048-160170358	K562	blood:	n/a	chr3:160170228-160170241 chr3:160170178-160170187
12	POLR2A	chr3:160170071-160170262	MCF-7	breast:	n/a	n/a
13	POLR2A	chr3:160169978-160170262	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:160170165-160170249	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:160169996-160170659	K562	blood:	n/a	n/a
16	HEY1	chr3:160170101-160170304	HepG2	liver:	n/a	n/a
17	MYC	chr3:160170133-160170259	MCF-7	breast:	n/a	n/a
18	POLR2A	chr3:160170152-160170325	A549	lung:	n/a	n/a
19	POLR2A	chr3:160170148-160170382	A549	lung:	n/a	n/a
20	POLR2A	chr3:160170075-160170260	GM12878	blood:	n/a	n/a
21	MYC	chr3:160170169-160170254	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr3:160170145-160170327	H1-hESC	embryonic stem cell:	n/a	n/a
23	CTCF	chr3:160170209-160170245	MCF-7	breast:	n/a	n/a
24	POLR2A	chr3:160169970-160170389	MCF-7	breast:	n/a	n/a
25	POLR2A	chr3:160169973-160170263	ProgFib	skin:	n/a	n/a
26	MYC	chr3:160170191-160170247	MCF-7	breast:	n/a	n/a
27	MAX	chr3:160170100-160170344	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr3:160170148-160170331	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:160170148-160170341	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr3:160170167-160170303	A549	lung:	n/a	n/a
31	POLR2A	chr3:160170051-160170584	MCF-7	breast:	n/a	n/a
32	POLR2A	chr3:160170034-160170268	HepG2	liver:	n/a	n/a
33	POLR2A	chr3:160169980-160170265	Gliobla	brain:	n/a	n/a
34	POLR2A	chr3:160170095-160170323	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:160170225-160170275	HCM	heart:	n/a
2	chr3:160170242-160170292	MCF10A-Er-Src	breast:	n/a
3	chr3:160170242-160170292	GM19239	blood:	n/a
4	chr3:160170225-160170275	ProgFib	skin:	n/a
5	chr3:160170242-160170292	HUVEC	blood vessel:	n/a
6	chr3:160170242-160170292	GM12878	blood:	n/a
7	chr3:160170242-160170292	K562	blood:	n/a
8	chr3:160170225-160170275	AG04449	skin:	fetal
9	chr3:160170225-160170275	Caco-2	colon:	n/a
10	chr3:160170225-160170275	MCF-7	breast:	n/a
11	chr3:160170225-160170275	AG10803	skin:	n/a
12	chr3:160170242-160170292	ECC-1	luminal epithelium:	n/a
13	chr3:160170242-160170292	Jurkat	blood:	n/a
14	chr3:160170242-160170292	AG10803	skin:	n/a
15	chr3:160170242-160170292	AG09319	gingival:	n/a
16	chr3:160170242-160170292	NH-A	brain:	n/a
17	chr3:160170225-160170275	HRPEpiC	eye:	n/a
18	chr3:160170242-160170292	BJ	skin:	n/a
19	chr3:160170242-160170292	NB4	blood:	n/a
20	chr3:160170242-160170292	HMEC	breast:	n/a
21	chr3:160170225-160170275	GM12892	blood:	n/a
22	chr3:160170242-160170292	PrEC	prostate:	n/a
23	chr3:160170225-160170275	HEK293	kidney:	embryo
24	chr3:160170225-160170275	A549	lung:	n/a
25	chr3:160170242-160170292	PFSK-1	brain:	n/a
26	chr3:160170225-160170275	SK-N-SH	brain:	n/a
27	chr3:160170225-160170275	LNCaP	prostate:	n/a
28	chr3:160170225-160170275	K562	blood:	n/a
29	chr3:160170242-160170292	GM06990	blood:	n/a
30	chr3:160170225-160170275	Hepatocyte	liver:	n/a
31	chr3:160170225-160170275	NT2-D1	testis:	n/a
32	chr3:160170225-160170275	PFSK-1	brain:	n/a
33	chr3:160170242-160170292	HPAEpiC	pulmonary alveolar:	n/a
34	chr3:160170242-160170292	SKMC	muscle:	n/a
35	chr3:160170242-160170292	BE2_C	brain:	n/a
36	chr3:160170242-160170292	MCF-7	breast:	n/a
37	chr3:160170242-160170292	NHBE	bronchial:	n/a
38	chr3:160170225-160170275	U87	brain:	n/a
39	chr3:160170225-160170275	AG09319	gingival:	n/a
40	chr3:160170242-160170292	PANC-1	pancreas:	n/a
41	chr3:160170225-160170275	RPTEC	kidney:	n/a
42	chr3:160170242-160170292	HRE	kidney:	n/a
43	chr3:160170242-160170292	HEEpiC	esophagus:	n/a
44	chr3:160170242-160170292	AG09309	skin:	n/a
45	chr3:160170242-160170292	U87	brain:	n/a
46	chr3:160170242-160170292	GM12892	blood:	n/a
47	chr3:160170242-160170292	AG04449	skin:	fetal
48	chr3:160170225-160170275	GM06990	blood:	n/a
49	chr3:160170225-160170275	HCT-116	colon:	n/a
50	chr3:160170242-160170292	AoSMC	blood vessel:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160164471..160170330-chr3:160281681..160284179,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000244009	TF binding region
ENSG00000248710	TF binding region
TRIM59	TF binding region
ENSG00000244009	CpG island
ENSG00000248710	CpG island
TRIM59	CpG island
ENSG00000229320	Chromatin interaction
ENSG00000186432	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10923	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10936201	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10936203	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11708118	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11709336	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11716413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11719750	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11720689	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11721112	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12152435	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12630770	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12630956	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12638633	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12639488	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16831207	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17236494	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17826137	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17826173	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17826257	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1873076	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1920663	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2095529	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2099496	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2275151	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3773369	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4679886	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679892	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4680581	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4680586	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56952700	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60395700	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6441311	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73875254	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73875259	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73875285	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73875290	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7644186	0.80[AMR][1000 genomes];0.81[EUR][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	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
rs12630564	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160168400-160172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:160168400-160172600	Weak transcription	Brain Substantia Nigra	brain
3	chr3:160168400-160172800	Weak transcription	Brain Anterior Caudate	brain
4	chr3:160169800-160171000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:160170200-160170400	Enhancers	Lung	lung
6	chr3:160170200-160171400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:160170200-160175600	Weak transcription	K562	blood

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