Variant report

Variant	rs3858586
Chromosome Location	chr12:49670489-49670490
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49670131-49670550	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr12:49664684-49670620	SK-N-MC	brain:	n/a	n/a
3	NR2F2	chr12:49669984-49671293	MCF-7	breast:	n/a	n/a
4	POLR2A	chr12:49670098-49670546	ECC-1	luminal epithelium:	n/a	n/a
5	GATA3	chr12:49670148-49670497	MCF-7	breast:	n/a	n/a
6	GATA3	chr12:49670029-49670586	MCF-7	breast:	n/a	n/a
7	CTCF	chr12:49670460-49670610	GM12867	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49670219..49671793-chr12:49739456..49742089,2	MCF-7	breast:
2	chr12:49667022..49671096-chr12:49685141..49687523,3	K562	blood:
3	chr12:49670426..49673698-chr12:49680662..49684493,5	K562	blood:
4	chr12:49667825..49672911-chr12:49731373..49736764,7	K562	blood:
5	chr12:49668999..49670991-chr12:49736933..49738497,2	K562	blood:
6	chr12:49666275..49670972-chr12:49688443..49691988,7	K562	blood:
7	chr12:49669514..49671024-chr12:49690193..49692290,2	MCF-7	breast:
8	chr12:49668500..49671128-chr12:49928861..49931681,2	MCF-7	breast:
9	chr12:49523127..49526155-chr12:49667398..49671055,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000258232	TF binding region
ENSG00000123416	Chromatin interaction
ENSG00000178401	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000135406	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10875941	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875942	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2335232	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858587	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49659200-49673600	Weak transcription	Fetal Brain Male	brain
2	chr12:49659600-49673600	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:49661600-49670600	Weak transcription	Psoas Muscle	Psoas
4	chr12:49662800-49673400	Weak transcription	Brain Anterior Caudate	brain
5	chr12:49662800-49673400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:49662800-49673400	Weak transcription	Brain Substantia Nigra	brain
7	chr12:49665200-49673200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:49665400-49673800	Weak transcription	Fetal Kidney	kidney
9	chr12:49665600-49673400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:49665600-49673400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:49666000-49670800	Weak transcription	Small Intestine	intestine
12	chr12:49666000-49673400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:49666800-49671200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:49667200-49673200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:49667400-49670600	Weak transcription	Hela-S3	cervix
16	chr12:49667400-49671000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr12:49667400-49671200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:49667400-49673400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:49667400-49673400	Weak transcription	Pancreas	Pancrea
20	chr12:49667600-49670800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:49667600-49673400	Weak transcription	Left Ventricle	heart
22	chr12:49667600-49673600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr12:49667800-49670600	Weak transcription	Liver	Liver
24	chr12:49667800-49670800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:49667800-49670800	Weak transcription	Dnd41	blood
26	chr12:49667800-49671200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:49667800-49671200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr12:49667800-49671200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:49667800-49671200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:49667800-49671400	Weak transcription	K562	blood
31	chr12:49667800-49673200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:49667800-49673200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr12:49667800-49673200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr12:49667800-49673400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:49667800-49673400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:49667800-49673400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:49667800-49673400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:49667800-49673400	Weak transcription	Esophagus	oesophagus
39	chr12:49667800-49673400	Weak transcription	Fetal Intestine Large	intestine
40	chr12:49668000-49671000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:49668000-49671000	Weak transcription	HUVEC	blood vessel
42	chr12:49668000-49671400	Weak transcription	Placenta	Placenta
43	chr12:49668000-49673400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr12:49668000-49673400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:49668000-49673400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:49668000-49673400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:49668000-49673400	Weak transcription	Fetal Brain Female	brain
48	chr12:49668000-49673600	Weak transcription	Fetal Lung	lung
49	chr12:49668000-49673800	Weak transcription	Adipose Nuclei	Adipose
50	chr12:49668000-49676000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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