Variant report

Variant	rs12065050
Chromosome Location	chr1:151222512-151222513
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151222444-151222513	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:151222117-151223495	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:151222016-151223768	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr1:151221846-151223889	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:151222355-151223278	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151222463..151229121-chr1:151253476..151256667,10	MCF-7	breast:
2	1:151219411-151234038..1:151592347-151603110	K562	blood:
3	chr1:151117703..151119369-chr1:151220283..151222884,2	K562	blood:
4	1:151171193-151178589..1:151219411-151234038	GM12878	blood:
5	chr1:151221893..151224459-chr1:151261973..151264497,2	K562	blood:
6	chr1:151215335..151217817-chr1:151220708..151223051,2	MCF-7	breast:
7	chr1:151031405..151033810-chr1:151221218..151224243,3	MCF-7	breast:
8	chr1:151222468..151224543-chr1:151225704..151227751,3	MCF-7	breast:
9	chr1:151221481..151225778-chr1:151225784..151229391,3	K562	blood:
10	chr1:151170978..151173263-chr1:151222128..151223645,2	MCF-7	breast:

No data

Variant related genes	Relation type
PSMD4	TF binding region
ENSG00000197622	Chromatin interaction
ENSG00000206635	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000143434	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11204788	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11204789	1.00[AMR][1000 genomes]
rs11204790	1.00[AMR][1000 genomes]
rs11204797	1.00[AMR][1000 genomes]
rs11204799	1.00[AMR][1000 genomes]
rs11204800	1.00[AMR][1000 genomes]
rs11204801	1.00[AMR][1000 genomes]
rs11204802	1.00[AMR][1000 genomes]
rs11204804	1.00[AMR][1000 genomes]
rs12057875	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12058806	1.00[AMR][1000 genomes]
rs12071605	1.00[AMR][1000 genomes]
rs12073695	1.00[AMR][1000 genomes]
rs12077026	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12077958	1.00[AMR][1000 genomes]
rs12080668	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12082248	1.00[AMR][1000 genomes]
rs12086389	1.00[AMR][1000 genomes]
rs12087802	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12090291	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12092749	1.00[AMR][1000 genomes]
rs12094954	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61751621	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9887870	1.00[AMR][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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151173200-151227200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:151178200-151223400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:151189600-151223600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:151190400-151223200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:151190400-151223400	Strong transcription	Fetal Thymus	thymus
6	chr1:151191800-151223000	Strong transcription	Fetal Stomach	stomach
7	chr1:151193400-151223000	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr1:151194400-151223600	Strong transcription	Fetal Muscle Trunk	muscle
9	chr1:151195000-151223000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:151195200-151227200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:151195600-151223000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:151195600-151223200	Strong transcription	Placenta	Placenta
13	chr1:151196000-151223200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:151196200-151222800	Strong transcription	Thymus	Thymus
15	chr1:151196200-151223200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:151196600-151222600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:151196600-151223200	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:151196800-151222800	Strong transcription	Fetal Muscle Leg	muscle
19	chr1:151197000-151222800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:151197000-151222800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:151197000-151223000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:151197200-151223200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:151197400-151223200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:151197400-151223600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:151199200-151222600	Strong transcription	Dnd41	blood
26	chr1:151199200-151223000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr1:151199400-151222600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:151199400-151222600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:151199400-151223000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:151199400-151223200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:151199600-151223200	Strong transcription	Liver	Liver
32	chr1:151199600-151223400	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr1:151199800-151223000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:151199800-151223200	Strong transcription	Adipose Nuclei	Adipose
35	chr1:151201400-151223200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:151202400-151223200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:151202400-151223200	Strong transcription	Brain Hippocampus Middle	brain
38	chr1:151202600-151223000	Strong transcription	Primary T cells from cord blood	blood
39	chr1:151202600-151223000	Strong transcription	Colon Smooth Muscle	Colon
40	chr1:151202600-151223000	Strong transcription	Left Ventricle	heart
41	chr1:151202600-151223200	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr1:151202800-151222800	Strong transcription	Fetal Lung	lung
43	chr1:151203000-151223400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:151203400-151223000	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr1:151203800-151222600	Strong transcription	Primary B cells from cord blood	blood
46	chr1:151206800-151226600	Weak transcription	Right Atrium	heart
47	chr1:151209400-151223000	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr1:151210200-151222800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr1:151210800-151223200	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr1:151211000-151223000	Strong transcription	Monocytes-CD14+_RO01746	blood

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