Variant report

Variant	rs12025638
Chromosome Location	chr1:153456349-153456350
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	chr1:153432889..153435323-chr1:153456139..153457737,2	MCF-7	breast:
2	chr1:153323483..153340048-chr1:153448254..153469845,61	MCF-7	breast:
3	chr1:153447398..153450153-chr1:153455745..153457768,2	MCF-7	breast:
4	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
5	chr1:153455880..153459414-chr1:153459858..153461522,3	MCF-7	breast:
6	chr1:153450588..153453299-chr1:153453645..153457534,3	MCF-7	breast:
7	chr1:153342148..153344034-chr1:153456102..153458087,3	MCF-7	breast:
8	chr1:153368085..153370692-chr1:153454166..153456468,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163220	Chromatin interaction
ENSG00000163218	Chromatin interaction
ENSG00000143556	Chromatin interaction
ENSG00000224784	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10888560	0.82[CHD][hapmap];0.81[YRI][hapmap]
rs11205297	1.00[ASW][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12021612	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022550	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][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]
rs12024114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12043280	1.00[ASW][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap]
rs12043556	0.94[YRI][hapmap]
rs12044034	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12047203	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12047494	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12217109	0.88[JPT][hapmap];0.92[YRI][hapmap]
rs16835332	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16835339	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28696717	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2986209	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55703007	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56009204	0.89[ASN][1000 genomes]
rs72708789	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
6	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12025638	RAB13	cis	cerebellum	SCAN
rs12025638	HORMAD1	cis	cerebellum	SCAN
rs12025638	LCE5A	cis	cerebellum	SCAN
rs12025638	LCE3D	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153451000-153467400	Weak transcription	Ovary	ovary
2	chr1:153451600-153456400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:153451800-153456400	Weak transcription	Fetal Heart	heart
4	chr1:153455400-153462200	Weak transcription	Right Ventricle	heart
5	chr1:153456200-153456400	Enhancers	Fetal Intestine Large	intestine
6	chr1:153456200-153456600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr1:153456200-153456800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr1:153456200-153456800	Enhancers	Placenta Amnion	Placenta Amnion
9	chr1:153456200-153456800	Bivalent Enhancer	Stomach Mucosa	stomach
10	chr1:153456200-153457000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:153456200-153457200	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr1:153456200-153457200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:153456200-153457200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:153456200-153457200	Enhancers	Fetal Muscle Leg	muscle
15	chr1:153456200-153457400	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:153456200-153457400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:153456200-153457600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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