Variant report

Variant	rs1872436
Chromosome Location	chr12:57322492-57322493
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:57321673..57323369-chr12:57347515..57349644,2	MCF-7	breast:
2	chr12:57315576..57318465-chr12:57319444..57323573,6	MCF-7	breast:
3	chr12:57321586..57325004-chr12:57326081..57330015,6	MCF-7	breast:
4	chr12:57257052..57259675-chr12:57321965..57323642,2	MCF-7	breast:
5	chr12:57321799..57323411-chr12:57480929..57483874,2	MCF-7	breast:
6	chr12:57316244..57318021-chr12:57321769..57323601,2	K562	blood:
7	chr12:57315724..57318021-chr12:57321769..57324066,3	K562	blood:
8	chr12:57322265..57324003-chr12:57330480..57332983,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000166881	Chromatin interaction
ENSG00000170426	Chromatin interaction
ENSG00000166886	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10506350	0.85[GIH][hapmap]
rs1072669	0.85[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs10876960	0.84[CHB][hapmap];0.84[ASN][1000 genomes]
rs11172071	0.82[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap]
rs11172072	0.86[ASN][1000 genomes]
rs11172076	0.81[ASN][1000 genomes]
rs1601405	0.85[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs17119173	0.82[JPT][hapmap]
rs17119301	0.82[GIH][hapmap]
rs1825514	0.81[CHD][hapmap];0.88[GIH][hapmap];0.84[ASN][1000 genomes]
rs2629413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782331	0.85[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs57926126	0.84[ASN][1000 genomes]
rs58009868	0.84[ASN][1000 genomes]
rs59665366	0.84[ASN][1000 genomes]
rs60101051	0.84[ASN][1000 genomes]
rs7136770	0.82[GIH][hapmap]
rs719749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs719750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7314055	0.88[JPT][hapmap]
rs7314151	0.85[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7314262	0.85[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7970701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs840163	0.85[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs844469	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs863459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs864541	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs901069	0.85[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.83[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	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv438213	chr12:57319810-57324496	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1872436	KRT75	cis	cerebellum	SCAN
rs1872436	MYL6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57316400-57326800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr12:57317400-57323400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:57317600-57323000	Weak transcription	Esophagus	oesophagus
4	chr12:57321200-57324000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:57321400-57325400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:57321400-57325400	Enhancers	K562	blood
7	chr12:57321400-57327200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:57321400-57328400	Enhancers	Fetal Thymus	thymus
9	chr12:57321600-57322600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr12:57321600-57323600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:57321800-57322600	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr12:57321800-57322800	Enhancers	Primary hematopoietic stem cells	blood
13	chr12:57322000-57328800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:57322200-57322600	Enhancers	H1 Cell Line	embryonic stem cell
15	chr12:57322200-57322600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr12:57322200-57322600	Enhancers	Fetal Kidney	kidney
17	chr12:57322200-57322800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:57322200-57322800	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr12:57322200-57325200	Weak transcription	Primary T cells from cord blood	blood
20	chr12:57322400-57322800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:57322400-57324800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr12:57322400-57325400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:57322400-57325400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:57322400-57325400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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