Variant report

Variant	rs12989778
Chromosome Location	chr2:178973029-178973030
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HMGN3	chr2:178972998-178973200	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:178973019-178973069	SK-N-SH_RA	brain:	n/a
2	chr2:178973019-178973069	NHBE	bronchial:	n/a
3	chr2:178973019-178973069	HRE	kidney:	n/a
4	chr2:178973019-178973069	AG04449	skin:	fetal
5	chr2:178973019-178973069	SAEC	small airway:	n/a
6	chr2:178973019-178973069	NT2-D1	testis:	n/a
7	chr2:178973019-178973069	GM12892	blood:	n/a
8	chr2:178973019-178973069	HNPCEpiC	eye:	n/a
9	chr2:178973019-178973069	A549	lung:	n/a
10	chr2:178973019-178973069	HEEpiC	esophagus:	n/a
11	chr2:178973019-178973069	HUVEC	blood vessel:	n/a
12	chr2:178973019-178973069	HRPEpiC	eye:	n/a
13	chr2:178973019-178973069	U87	brain:	n/a
14	chr2:178973019-178973069	H1-hESC	embryonic stem cell:	embryo
15	chr2:178973019-178973069	GM12878	blood:	n/a
16	chr2:178973019-178973069	MCF10A-Er-Src	breast:	n/a
17	chr2:178973019-178973069	K562	blood:	n/a
18	chr2:178973019-178973069	RPTEC	kidney:	n/a
19	chr2:178973019-178973069	ECC-1	luminal epithelium:	n/a
20	chr2:178973019-178973069	HRCEpiC	kidney:	n/a
21	chr2:178973019-178973069	Hepatocyte	liver:	n/a
22	chr2:178973019-178973069	SK-N-MC	brain:	n/a
23	chr2:178973019-178973069	HCT-116	colon:	n/a
24	chr2:178973019-178973069	Hela-S3	cervix:	n/a
25	chr2:178973019-178973069	NH-A	brain:	n/a
26	chr2:178973019-178973069	T-47D	breast:	n/a
27	chr2:178973019-178973069	PrEC	prostate:	n/a
28	chr2:178973019-178973069	CMK	blood:	n/a
29	chr2:178973019-178973069	NB4	blood:	n/a
30	chr2:178973019-178973069	HCPEpiC	choroid plexus:	n/a
31	chr2:178973019-178973069	NHDF-neo	bronchial:	n/a
32	chr2:178973019-178973069	AG04450	lung:	fetal
33	chr2:178973019-178973069	PFSK-1	brain:	n/a
34	chr2:178973019-178973069	SKMC	muscle:	n/a
35	chr2:178973019-178973069	HL-60	blood:	n/a
36	chr2:178973019-178973069	AG09309	skin:	n/a
37	chr2:178973019-178973069	HIPEpiC	eye:	n/a
38	chr2:178973019-178973069	GM12891	blood:	n/a
39	chr2:178973019-178973069	PANC-1	pancreas:	n/a
40	chr2:178973019-178973069	HEK293	kidney:	embryo
41	chr2:178973019-178973069	GM19239	blood:	n/a
42	chr2:178973019-178973069	BE2_C	brain:	n/a
43	chr2:178973019-178973069	ovcar-3	ovarian:	n/a
44	chr2:178973019-178973069	HepG2	liver:	n/a
45	chr2:178973019-178973069	GM06990	blood:	n/a
46	chr2:178973019-178973069	HCF	heart:	n/a
47	chr2:178973019-178973069	AG09319	gingival:	n/a
48	chr2:178973019-178973069	AoSMC	blood vessel:	n/a
49	chr2:178973019-178973069	Caco-2	colon:	n/a
50	chr2:178973019-178973069	HPAEpiC	pulmonary alveolar:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178970656..178974678-chr2:178975520..178979270,3	K562	blood:
2	chr2:178972756..178975132-chr2:178975866..178978416,2	MCF-7	breast:

No data

Variant related genes	Relation type
CYCTP	TF binding region
RBM45	TF binding region
RBM45	CpG island
CYCTP	CpG island
ENSG00000155636	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12987593	1.00[CEU][hapmap]
rs12989423	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12993389	1.00[AFR][1000 genomes]
rs13013828	1.00[CEU][hapmap]
rs13022267	1.00[AFR][1000 genomes]
rs13023049	1.00[AFR][1000 genomes]
rs13023495	1.00[AFR][1000 genomes]
rs13026481	1.00[AFR][1000 genomes]
rs13027582	1.00[AFR][1000 genomes]
rs13028692	1.00[AFR][1000 genomes]
rs13033194	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419755	1.00[ASN][1000 genomes]
rs17330381	1.00[AFR][1000 genomes]
rs17635803	1.00[AFR][1000 genomes]
rs17635875	1.00[AFR][1000 genomes]
rs17635934	1.00[AFR][1000 genomes]
rs17635957	1.00[AFR][1000 genomes]
rs17687170	1.00[AFR][1000 genomes]
rs17687217	1.00[AFR][1000 genomes]
rs2056715	1.00[AFR][1000 genomes]
rs334055	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334060	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334064	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334065	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334071	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334076	1.00[ASN][1000 genomes]
rs334077	1.00[ASN][1000 genomes]
rs34018298	1.00[AFR][1000 genomes]
rs34069002	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34234621	1.00[AFR][1000 genomes]
rs34395717	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34406776	1.00[AFR][1000 genomes]
rs34702539	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34927879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35286879	1.00[AFR][1000 genomes]
rs35454650	1.00[AFR][1000 genomes]
rs35591668	1.00[AFR][1000 genomes]
rs35620189	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35938761	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737266	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71423535	1.00[AFR][1000 genomes]
rs71423537	1.00[AFR][1000 genomes]
rs71423538	1.00[AFR][1000 genomes]
rs71423540	1.00[AFR][1000 genomes]
rs71423553	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71423554	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71423555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv583739	chr2:178942302-178993562	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv518790	chr2:178963445-179000291	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178971200-178976800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:178973000-178973200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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