Variant report

Variant	rs2329842
Chromosome Location	chr21:46086868-46086869
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HA-E2F1	chr21:46086500-46087069	MCF-7	breast:	n/a	n/a
2	MYC	chr21:46086621-46086896	MCF-7	breast:	n/a	n/a
3	MYC	chr21:46086673-46086931	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr21:46086674-46087163	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr21:46086434-46086917	MCF-7	breast:	n/a	n/a
6	MYC	chr21:46086389-46086888	MCF-7	breast:	n/a	n/a
7	POLR2A	chr21:46086301-46086896	MCF-7	breast:	n/a	n/a
8	MYC	chr21:46086671-46086937	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr21:46086629-46087212	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr21:46086733-46087171	MCF10A-Er-Src	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr21:46086855-46086905	HRE	kidney:	n/a
2	chr21:46086855-46086905	NHBE	bronchial:	n/a
3	chr21:46086855-46086905	SKMC	muscle:	n/a
4	chr21:46086855-46086905	HPAEpiC	pulmonary alveolar:	n/a
5	chr21:46086855-46086905	HepG2	liver:	n/a
6	chr21:46086855-46086905	IMR90	lung:	fetal
7	chr21:46086855-46086905	LNCaP	prostate:	n/a
8	chr21:46086855-46086905	RPTEC	kidney:	n/a
9	chr21:46086855-46086905	AG09309	skin:	n/a
10	chr21:46086855-46086905	GM06990	blood:	n/a
11	chr21:46086855-46086905	ECC-1	luminal epithelium:	n/a
12	chr21:46086855-46086905	HRCEpiC	kidney:	n/a
13	chr21:46086855-46086905	Hepatocyte	liver:	n/a
14	chr21:46086855-46086905	HL-60	blood:	n/a
15	chr21:46086855-46086905	MCF-7	breast:	n/a
16	chr21:46086855-46086905	HAEpiC	amniotic membrane:	n/a
17	chr21:46086855-46086905	CMK	blood:	n/a
18	chr21:46086855-46086905	HCM	heart:	n/a
19	chr21:46086855-46086905	MCF10A-Er-Src	breast:	n/a
20	chr21:46086855-46086905	BJ	skin:	n/a
21	chr21:46086855-46086905	HEK293	kidney:	embryo
22	chr21:46086855-46086905	Hela-S3	cervix:	n/a
23	chr21:46086855-46086905	NT2-D1	testis:	n/a
24	chr21:46086855-46086905	BE2_C	brain:	n/a
25	chr21:46086855-46086905	ovcar-3	ovarian:	n/a
26	chr21:46086855-46086905	HEEpiC	esophagus:	n/a
27	chr21:46086855-46086905	SAEC	small airway:	n/a
28	chr21:46086855-46086905	T-47D	breast:	n/a
29	chr21:46086855-46086905	AG10803	skin:	n/a
30	chr21:46086855-46086905	AG04449	skin:	fetal
31	chr21:46086855-46086905	ProgFib	skin:	n/a
32	chr21:46086855-46086905	K562	blood:	n/a
33	chr21:46086855-46086905	HRPEpiC	eye:	n/a
34	chr21:46086855-46086905	SK-N-SH_RA	brain:	n/a
35	chr21:46086855-46086905	U87	brain:	n/a
36	chr21:46086855-46086905	HIPEpiC	eye:	n/a
37	chr21:46086855-46086905	GM12892	blood:	n/a
38	chr21:46086855-46086905	GM12891	blood:	n/a
39	chr21:46086855-46086905	NH-A	brain:	n/a
40	chr21:46086855-46086905	HMEC	breast:	n/a
41	chr21:46086855-46086905	GM19239	blood:	n/a
42	chr21:46086855-46086905	NHDF-neo	bronchial:	n/a
43	chr21:46086855-46086905	NB4	blood:	n/a
44	chr21:46086855-46086905	AoSMC	blood vessel:	n/a
45	chr21:46086855-46086905	HUVEC	blood vessel:	n/a
46	chr21:46086855-46086905	A549	lung:	n/a
47	chr21:46086855-46086905	Jurkat	blood:	n/a
48	chr21:46086855-46086905	PANC-1	pancreas:	n/a
49	chr21:46086855-46086905	PFSK-1	brain:	n/a
50	chr21:46086855-46086905	HCPEpiC	choroid plexus:	n/a

No data

Variant related genes	Relation type
KRTAP12-2	TF binding region
KRTAP12-2	CpG island

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10854463	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12106369	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12482870	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13046903	0.80[ASN][1000 genomes]
rs1883039	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1883041	0.96[ASN][1000 genomes]
rs2073437	0.87[ASN][1000 genomes]
rs2210284	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2225433	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2256361	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2256490	0.97[ASN][1000 genomes]
rs2256496	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329838	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329839	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329840	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329841	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329843	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838614	0.90[ASN][1000 genomes]
rs2838617	0.91[ASN][1000 genomes]
rs2838618	0.91[ASN][1000 genomes]
rs2838619	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2838623	0.95[ASN][1000 genomes]
rs2838624	0.96[ASN][1000 genomes]
rs2838625	0.96[ASN][1000 genomes]
rs2838627	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34979768	0.91[ASN][1000 genomes]
rs35163632	0.80[ASN][1000 genomes]
rs3966427	0.82[ASN][1000 genomes]
rs4818728	0.82[ASN][1000 genomes]
rs4818953	0.90[ASN][1000 genomes]
rs7275203	0.91[ASN][1000 genomes]
rs7275666	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7277758	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7282198	0.84[EUR][1000 genomes]
rs7282421	0.91[ASN][1000 genomes]
rs926193	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9306111	0.91[ASN][1000 genomes]
rs9306112	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9974195	0.89[ASN][1000 genomes]
rs9983049	0.91[ASN][1000 genomes]
rs9983892	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065798	chr21:45941000-46097463	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv869108	chr21:45941000-46097463	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv544476	chr21:45941000-46097463	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv913950	chr21:45985068-46097463	Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46079400-46089600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr21:46086400-46087000	Enhancers	Esophagus	oesophagus
3	chr21:46086400-46087000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr21:46086600-46087000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr21:46086800-46087000	Enhancers	Hela-S3	cervix
6	chr21:46086800-46087200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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