Variant report

Variant	rs10023472
Chromosome Location	chr4:644410-644411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:636743..639513-chr4:642400..644519,2	MCF-7	breast:
2	chr4:642830..644425-chr4:665822..667972,2	K562	blood:
3	chr4:644054..646414-chr4:656838..659721,2	MCF-7	breast:
4	chr4:642131..644821-chr4:649750..652284,2	MCF-7	breast:
5	chr4:644162..647846-chr4:649268..652076,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215375	Chromatin interaction
ENSG00000242686	Chromatin interaction
ENSG00000133256	Chromatin interaction
ENSG00000169020	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10007206	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10007497	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10011154	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10021714	0.84[CHD][hapmap]
rs10027866	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[ASN][1000 genomes]
rs10029928	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10031745	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[ASN][1000 genomes]
rs10031968	0.94[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs11248029	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13107358	0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs28374488	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.99[ASN][1000 genomes]
rs28380593	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28403281	0.88[ASN][1000 genomes]
rs28438498	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.99[ASN][1000 genomes]
rs28470912	0.85[LWK][hapmap];0.86[MKK][hapmap]
rs28476575	0.94[ASN][1000 genomes]
rs28502612	0.84[ASN][1000 genomes]
rs28504161	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28520978	0.82[ASN][1000 genomes]
rs28569875	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28588872	1.00[ASN][1000 genomes]
rs28600205	0.99[ASN][1000 genomes]
rs28714509	0.88[ASN][1000 genomes]
rs28754797	0.94[ASN][1000 genomes]
rs28769407	0.88[ASN][1000 genomes]
rs28826275	0.88[ASN][1000 genomes]
rs34307246	0.88[ASN][1000 genomes]
rs3864130	0.81[MKK][hapmap]
rs3888807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3934459	0.83[ASN][1000 genomes]
rs4075653	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4463020	0.85[LWK][hapmap];0.86[MKK][hapmap]
rs4505760	1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs59623849	0.93[ASN][1000 genomes]
rs67030464	0.99[ASN][1000 genomes]
rs67703486	0.94[ASN][1000 genomes]
rs72611195	0.81[ASN][1000 genomes]
rs72611197	0.87[ASN][1000 genomes]
rs72611198	0.88[ASN][1000 genomes]
rs72611199	0.88[ASN][1000 genomes]
rs72611200	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72611201	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72611202	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72613103	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72613104	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72613105	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72613106	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72613107	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72613108	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7438471	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7661376	0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs9884240	0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs9997286	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9998967	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
9	nsv878246	chr4:592507-696848	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
14	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
15	nsv593207	chr4:629437-645300	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
16	nsv4194	chr4:635316-657212	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10023472	POLN	cis	parietal	SCAN
rs10023472	ZNF721	cis	parietal	SCAN
rs10023472	MFSD7	cis	Esophagus Muscularis	GTEx
rs10023472	ZNF141	cis	cerebellum	SCAN
rs10023472	MYOZ3	trans	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:631400-657000	Weak transcription	Right Atrium	heart
2	chr4:640400-648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:641800-657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:642200-652800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:642400-654600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:642600-645000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:642800-644600	Weak transcription	Gastric	stomach
8	chr4:642800-657000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:643000-646000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr4:643000-657000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr4:643200-646200	Bivalent Enhancer	Fetal Muscle Leg	muscle
12	chr4:643200-648200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:643400-644600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:643600-644600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr4:644000-645200	Enhancers	Brain Substantia Nigra	brain
16	chr4:644200-644600	Enhancers	Brain Angular Gyrus	brain
17	chr4:644200-644600	Enhancers	Brain Anterior Caudate	brain
18	chr4:644200-645000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:644400-644600	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr4:644400-644600	Flanking Active TSS	Right Ventricle	heart
21	chr4:644400-644600	Bivalent Enhancer	HepG2	liver
22	chr4:644400-644800	Enhancers	Brain Hippocampus Middle	brain
23	chr4:644400-645000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:644400-645200	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
25	chr4:644400-645400	Enhancers	Fetal Heart	heart
26	chr4:644400-646000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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