Variant report

Variant	rs4336286
Chromosome Location	chr4:55843059-55843060
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:75)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:75 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:55843000-55843150	HFF-Myc	foreskin:	n/a	n/a
2	RAD21	chr4:55842896-55843174	HepG2	liver:	n/a	n/a
3	CTCF	chr4:55843020-55843170	AG04449	skin:	n/a	n/a
4	CTCF	chr4:55842960-55843110	HEEpiC	esophagus:	n/a	n/a
5	CTCF	chr4:55842940-55843090	HEK293	kidney:	n/a	n/a
6	RAD21	chr4:55842928-55843121	K562	blood:	n/a	n/a
7	ZNF143	chr4:55842923-55843137	K562	blood:	n/a	n/a
8	RAD21	chr4:55842938-55843228	ECC-1	luminal epithelium:	n/a	n/a
9	RAD21	chr4:55842735-55843342	HCT-116	colon:	n/a	n/a
10	CTCF	chr4:55842960-55843106	NHEK	skin:	n/a	n/a
11	RAD21	chr4:55842906-55843167	MCF-7	breast:	n/a	n/a
12	CTCF	chr4:55842940-55843090	WERI-Rb-1	eye:	n/a	n/a
13	CTCF	chr4:55842920-55843132	A549	lung:	n/a	n/a
14	CTCF	chr4:55842878-55843243	K562	blood:	n/a	n/a
15	CTCF	chr4:55842980-55843130	MCF-7	breast:	n/a	n/a
16	ZNF263	chr4:55842863-55843391	HEK293-T-REx	kidney:	n/a	n/a
17	CTCF	chr4:55842807-55843217	K562	blood:	n/a	n/a
18	CTCF	chr4:55842960-55843110	A549	lung:	n/a	n/a
19	CTCF	chr4:55842960-55843110	HMEC	breast:	n/a	n/a
20	CTCF	chr4:55842960-55843110	HepG2	liver:	n/a	n/a
21	CTCF	chr4:55842846-55843216	K562	blood:	n/a	n/a
22	CTCF	chr4:55842934-55843138	MCF-7	breast:	n/a	n/a
23	CTCF	chr4:55842927-55843182	H1-hESC	embryonic stem cell:	n/a	n/a
24	RAD21	chr4:55842859-55843168	HepG2	liver:	n/a	n/a
25	CTCF	chr4:55842876-55843261	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr4:55842960-55843110	HBMEC	blood vessel:	n/a	n/a
27	CTCF	chr4:55843020-55843170	K562	blood:	n/a	n/a
28	CTCF	chr4:55842960-55843110	HCFaa	heart:	n/a	n/a
29	RAD21	chr4:55842771-55843249	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr4:55842960-55843110	GM12873	blood:	n/a	n/a
31	CTCF	chr4:55843000-55843150	HCM	heart:	n/a	n/a
32	CTCF	chr4:55842940-55843090	A549	lung:	n/a	n/a
33	CTCF	chr4:55842920-55843070	MCF-7	breast:	n/a	n/a
34	CTCF	chr4:55843000-55843150	Hela-S3	cervix:	n/a	n/a
35	CTCF	chr4:55842721-55843284	H1-hESC	embryonic stem cell:	n/a	n/a
36	RAD21	chr4:55842936-55843116	K562	blood:	n/a	n/a
37	CTCF	chr4:55842940-55843090	HCT-116	colon:	n/a	n/a
38	CTCF	chr4:55842960-55843110	WERI-Rb-1	eye:	n/a	n/a
39	CTCF	chr4:55842894-55843181	MCF-7	breast:	n/a	n/a
40	CTCF	chr4:55842955-55843111	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr4:55842906-55843116	T-47D	breast:	n/a	n/a
42	ZNF143	chr4:55842876-55843219	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr4:55842886-55843139	HepG2	liver:	n/a	n/a
44	CTCF	chr4:55842960-55843110	SAEC	small airway:	n/a	n/a
45	RAD21	chr4:55842753-55843309	H1-hESC	embryonic stem cell:	n/a	n/a
46	SMC3	chr4:55842966-55843077	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr4:55842960-55843110	HCPEpiC	choroid plexus:	n/a	n/a
48	CTCF	chr4:55842960-55843110	NHEK	skin:	n/a	n/a
49	RAD21	chr4:55842895-55843156	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr4:55842916-55843164	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:55841032..55843418-chr4:55929631..55932494,2	K562	blood:
2	chr4:55842594..55843356-chr4:56187739..56188757,3	MCF-7	breast:

No data

Variant related genes	Relation type
RPL38P3	TF binding region
ENSG00000244034	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1075065	0.98[ASN][1000 genomes]
rs11941928	0.90[ASN][1000 genomes]
rs12502309	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12640896	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13101326	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13101685	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13101777	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13104623	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106311	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13110915	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13111813	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13111838	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13114647	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13125964	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13126022	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13126236	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13127180	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13127753	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13129153	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130324	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13138898	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13144612	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146834	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4259115	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4317261	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4320192	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4334808	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4337782	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356964	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4524450	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4569809	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4599477	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57266861	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61696777	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554219	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6554222	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554223	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820549	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6821744	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6822352	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6824426	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6826834	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71624987	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7657044	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667898	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv948758	chr4:55748430-55887962	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv829938	chr4:55836964-55857893	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4336286	RPL21P44	cis	parietal	SCAN
rs4336286	SCFD2	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55838400-55843200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr4:55842800-55843400	Enhancers	H1 Cell Line	embryonic stem cell
3	chr4:55842800-55843400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr4:55842800-55843800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr4:55842800-55843800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:55842800-55844400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:55843000-55843400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr4:55843000-55843400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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