Variant report

Variant	rs3858675
Chromosome Location	chr12:63330004-63330005
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	FOXA1	chr12:63329820-63330191	T-47D	breast:	n/a	n/a
2	FOXA1	chr12:63329908-63330198	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
PPM1H	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10506468	0.88[EUR][1000 genomes]
rs11174723	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11174731	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12301080	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12302398	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12302449	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12304611	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12311870	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12314057	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12315582	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12316918	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1250152	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1666909	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1681992	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1681993	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1681994	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1695023	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17098649	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1731665	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2173441	0.96[ASN][1000 genomes]
rs2442110	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2628036	0.96[ASN][1000 genomes]
rs2628038	0.98[ASN][1000 genomes]
rs3858674	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58389317	0.88[EUR][1000 genomes]
rs58869921	0.88[EUR][1000 genomes]
rs699587	0.88[EUR][1000 genomes]
rs7314488	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7314892	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315141	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3415227	chr12:63228121-63591615	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv899162	chr12:63279750-63334242	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	esv3355722	chr12:63327210-63330258	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	esv3378901	chr12:63327535-63330133	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63329200-63330200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr12:63329400-63330200	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr12:63329400-63330400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:63329400-63334000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:63329400-63335200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:63329400-63335200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr12:63329400-63335200	Weak transcription	Brain Anterior Caudate	brain
8	chr12:63329600-63330200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr12:63329600-63330200	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr12:63329600-63330600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr12:63329600-63338600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:63329800-63330600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr12:63329800-63330800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr12:63329800-63334800	Weak transcription	Brain Substantia Nigra	brain
15	chr12:63329800-63335400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:63330000-63330200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:63330000-63330200	Enhancers	H9 Cell Line	embryonic stem cell
18	chr12:63330000-63330200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:63330000-63330200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
20	chr12:63330000-63330200	Enhancers	Brain Angular Gyrus	brain
21	chr12:63330000-63330200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr12:63330000-63330400	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr12:63330000-63330600	Enhancers	Pancreatic Islets	Pancreatic Islet

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