Variant report

Variant	rs12746499
Chromosome Location	chr1:184354199-184354200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:184353636-184354785	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:184349850..184351916-chr1:184352544..184355292,2	K562	blood:
2	chr1:184353036..184355475-chr1:184360672..184362232,2	MCF-7	breast:
3	chr1:184354030..184359077-chr1:184375771..184381189,10	MCF-7	breast:

Variant related genes	Relation type
C1orf21	TF binding region
ENSG00000230470	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10911556	1.00[CHD][hapmap]
rs10911582	1.00[ASN][1000 genomes]
rs12082456	1.00[ASN][1000 genomes]
rs12083933	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12096575	1.00[CHD][hapmap]
rs12723932	1.00[ASN][1000 genomes]
rs12726204	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12727991	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12735278	1.00[ASN][1000 genomes]
rs12735902	1.00[ASN][1000 genomes]
rs12743066	1.00[ASN][1000 genomes]
rs12743488	1.00[ASN][1000 genomes]
rs12754557	1.00[ASN][1000 genomes]
rs12756084	0.88[EUR][1000 genomes]
rs12756319	1.00[ASN][1000 genomes]
rs13374607	1.00[GIH][hapmap]
rs13374609	1.00[ASN][1000 genomes]
rs1547608	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856561	1.00[ASN][1000 genomes]
rs1930293	1.00[CHD][hapmap]
rs1970391	1.00[ASN][1000 genomes]
rs2180075	1.00[ASN][1000 genomes]
rs34072105	1.00[ASN][1000 genomes]
rs34282348	0.84[EUR][1000 genomes]
rs34312759	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34418556	1.00[ASN][1000 genomes]
rs34427261	1.00[ASN][1000 genomes]
rs34579903	1.00[ASN][1000 genomes]
rs34591137	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34712320	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34946851	1.00[ASN][1000 genomes]
rs35021091	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35040136	1.00[ASN][1000 genomes]
rs35350002	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35414247	1.00[ASN][1000 genomes]
rs35430213	1.00[ASN][1000 genomes]
rs35782682	1.00[ASN][1000 genomes]
rs35901887	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35964209	0.88[EUR][1000 genomes]
rs35999930	1.00[ASN][1000 genomes]
rs3886022	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4275415	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4332324	1.00[ASN][1000 genomes]
rs4354508	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4390140	1.00[ASN][1000 genomes]
rs4466608	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650665	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650668	1.00[ASN][1000 genomes]
rs4650669	1.00[ASN][1000 genomes]
rs4651204	1.00[ASN][1000 genomes]
rs4651207	1.00[GIH][hapmap]
rs4651212	1.00[ASN][1000 genomes]
rs4651222	1.00[ASN][1000 genomes]
rs59079733	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659461	0.98[EUR][1000 genomes]
rs66916459	1.00[ASN][1000 genomes]
rs68054616	1.00[ASN][1000 genomes]
rs71634105	1.00[ASN][1000 genomes]
rs71634106	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71634108	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71634109	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74131654	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74131659	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531736	1.00[ASN][1000 genomes]
rs9970629	1.00[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	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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	21 gene(s)	inside rSNPs	diseases
2	nsv3821	chr1:184319543-184365236	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184337400-184355000	Weak transcription	Psoas Muscle	Psoas
2	chr1:184346000-184355000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:184346200-184355000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:184348400-184355000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:184348800-184355000	Weak transcription	Fetal Heart	heart
6	chr1:184348800-184355000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:184349000-184355000	Weak transcription	NHLF	lung
8	chr1:184350400-184355000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:184350400-184355000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:184350600-184354600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:184350600-184355000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:184351800-184354600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr1:184351800-184354800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:184352000-184354400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr1:184352200-184354400	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:184352200-184355000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:184353200-184354200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:184353600-184354200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr1:184353800-184354600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:184353800-184354600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
21	chr1:184353800-184354800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:184354000-184354600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr1:184354000-184355000	Enhancers	H9 Cell Line	embryonic stem cell
24	chr1:184354000-184355000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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