Variant report

Variant	rs456993
Chromosome Location	chr6:33358278-33358279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZC3H11A	chr6:33358173-33359455	K562	blood:	n/a	n/a
2	RFX5	chr6:33358003-33360752	SK-N-SH	brain:	n/a	n/a
3	JUN	chr6:33358175-33360477	K562	blood:	n/a	n/a

No data

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:33357200..33360290-chr6:33405779..33409122,3	K562	blood:
2	chr6:33279220..33282454-chr6:33357653..33360404,5	MCF-7	breast:
3	chr6:33356706..33359588-chr6:33384249..33386179,3	MCF-7	breast:
4	chr6:33357638..33360083-chr6:33386720..33388943,3	MCF-7	breast:
5	chr6:33237283..33241357-chr6:33358017..33360541,6	K562	blood:
6	chr6:33356382..33361019-chr6:33384058..33388661,8	K562	blood:
7	chr6:33281855..33283498-chr6:33357981..33360061,3	MCF-7	breast:
8	chr6:33283316..33288344-chr6:33357863..33362367,8	K562	blood:
9	chr6:33357335..33362175-chr6:33383352..33389421,14	K562	blood:
10	chr6:33239039..33242495-chr6:33357243..33362134,5	MCF-7	breast:
11	chr6:33264068..33267385-chr6:33357975..33361447,5	MCF-7	breast:
12	chr6:33358270..33361160-chr6:33397889..33401606,4	K562	blood:
13	chr6:33357351..33361150-chr6:33373102..33380127,12	MCF-7	breast:
14	chr6:33285348..33292496-chr6:33357328..33361566,13	K562	blood:
15	chr6:33238428..33241280-chr6:33357854..33362793,6	MCF-7	breast:
16	chr6:33358222..33360525-chr6:33377821..33380717,3	MCF-7	breast:
17	chr6:33237283..33247485-chr6:33356185..33362256,17	K562	blood:
18	chr6:33264179..33271329-chr6:33356528..33360865,9	K562	blood:
19	chr6:33256540..33259907-chr6:33358017..33361464,3	MCF-7	breast:
20	chr6:33283943..33291558-chr6:33357867..33362243,10	MCF-7	breast:
21	chr6:33243431..33246571-chr6:33357252..33359910,3	MCF-7	breast:
22	chr6:33243392..33248315-chr6:33357393..33361975,11	K562	blood:
23	chr6:33280708..33283139-chr6:33358214..33362149,5	K562	blood:
24	chr6:33253660..33257073-chr6:33358023..33361324,4	K562	blood:
25	chr6:33356271..33363521-chr6:33371085..33380351,32	K562	blood:
26	chr6:33357884..33361160-chr6:33397889..33401606,5	K562	blood:
27	chr6:33283728..33287391-chr6:33357794..33361686,6	MCF-7	breast:
28	chr6:33265384..33269852-chr6:33356528..33361842,9	K562	blood:

No data

Variant related genes	Relation type
RPL35AP4	TF binding region
KIFC1	TF binding region
ENSG00000227057	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000264085	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000204220	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000223501	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000231500	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11757273	0.85[ASN][1000 genomes]
rs12204193	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1613451	0.88[ASN][1000 genomes]
rs1755047	0.88[ASN][1000 genomes]
rs2274730	0.90[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2480487	0.86[ASN][1000 genomes]
rs2743	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2772373	0.90[ASN][1000 genomes]
rs2772387	0.85[ASN][1000 genomes]
rs2772390	0.86[ASN][1000 genomes]
rs2772392	0.86[ASN][1000 genomes]
rs3117320	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3130001	0.83[EUR][1000 genomes]
rs3130002	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3130006	0.82[AMR][1000 genomes]
rs3130007	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3130015	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3130025	0.86[ASN][1000 genomes]
rs3130274	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3130275	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3130276	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs371005	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs376006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs391500	0.89[AMR][1000 genomes]
rs420714	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs442745	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs459927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs461887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs461964	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4620113	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs465223	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs465474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs465506	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs465877	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs467065	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66840884	0.84[ASN][1000 genomes]
rs6942045	0.88[AMR][1000 genomes]
rs9278025	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9278029	0.87[AMR][1000 genomes]
rs9357159	0.84[ASN][1000 genomes]
rs9368760	0.85[AMR][1000 genomes]
rs9380355	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380365	0.84[CHB][hapmap]
rs9461856	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs456993	CDKN1A	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33341200-33358600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:33343800-33359200	Weak transcription	Right Atrium	heart
3	chr6:33345600-33358800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:33348400-33358800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:33351800-33358600	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:33352600-33358800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:33352800-33358400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:33352800-33358400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:33352800-33358400	Weak transcription	Hela-S3	cervix
10	chr6:33352800-33358400	Weak transcription	HepG2	liver
11	chr6:33352800-33358800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:33352800-33358800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:33352800-33358800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:33352800-33358800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:33353200-33358400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:33354800-33358600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:33357400-33358400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:33358000-33358600	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr6:33358000-33358800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr6:33358200-33358400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr6:33358200-33358400	Enhancers	Dnd41	blood
22	chr6:33358200-33358400	Enhancers	K562	blood
23	chr6:33358200-33358600	Enhancers	Primary T cells from cord blood	blood
24	chr6:33358200-33358600	Enhancers	Primary T cells fromperipheralblood	blood
25	chr6:33358200-33358600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr6:33358200-33358600	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr6:33358200-33358600	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr6:33358200-33358600	Enhancers	GM12878-XiMat	blood
29	chr6:33358200-33358800	Enhancers	Primary B cells from peripheral blood	blood
30	chr6:33358200-33358800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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