Variant report

Variant	rs12231444
Chromosome Location	chr12:124074365-124074366
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	POLR2A	chr12:124074315-124074841	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:124017908..124019727-chr12:124073877..124075658,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247373	TF binding region
ENSG00000188026	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10161548	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773019	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773020	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10773023	0.81[EUR][1000 genomes]
rs10773024	0.81[EUR][1000 genomes]
rs10773025	0.81[EUR][1000 genomes]
rs10846530	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846532	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846534	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10846536	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10846538	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10846539	0.81[EUR][1000 genomes]
rs10846542	0.81[EUR][1000 genomes]
rs10846543	0.81[EUR][1000 genomes]
rs10846545	0.81[EUR][1000 genomes]
rs11057299	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057300	0.81[ASN][1000 genomes]
rs11057301	0.81[ASN][1000 genomes]
rs11057304	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057310	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057312	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11057313	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11057322	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11057329	0.81[EUR][1000 genomes]
rs11057331	0.81[EUR][1000 genomes]
rs11057332	0.81[EUR][1000 genomes]
rs11057336	0.81[EUR][1000 genomes]
rs11572926	0.85[ASN][1000 genomes]
rs11572940	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11572949	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12308953	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309685	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313119	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17840832	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2292702	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2707	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34369761	0.81[ASN][1000 genomes]
rs3704	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748270	0.87[ASN][1000 genomes]
rs3748271	0.81[EUR][1000 genomes]
rs3850952	0.81[ASN][1000 genomes]
rs3923720	0.87[ASN][1000 genomes]
rs4930713	0.81[ASN][1000 genomes]
rs4930714	0.81[ASN][1000 genomes]
rs61154946	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488887	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7298287	0.92[ASN][1000 genomes]
rs7302177	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7303409	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7307219	0.81[EUR][1000 genomes]
rs7311689	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7316410	0.87[ASN][1000 genomes]
rs73414223	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7358562	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967780	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7972380	0.81[ASN][1000 genomes]
rs9919	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
6	esv2422416	chr12:124009676-124085689	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 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	chr12:124070000-124085800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:124070400-124076400	Weak transcription	Ovary	ovary
3	chr12:124070400-124076600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:124070600-124082200	Strong transcription	Fetal Muscle Leg	muscle
5	chr12:124070600-124084400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:124070800-124074600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
7	chr12:124070800-124077200	Genic enhancers	HUVEC	blood vessel
8	chr12:124071000-124077400	Genic enhancers	HepG2	liver
9	chr12:124071200-124075200	Strong transcription	Fetal Kidney	kidney
10	chr12:124071200-124075400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:124071200-124077200	Strong transcription	Fetal Lung	lung
12	chr12:124071200-124077400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:124071200-124082800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:124071200-124083400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:124071200-124083400	Strong transcription	Fetal Intestine Large	intestine
16	chr12:124071200-124083600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr12:124071200-124083600	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr12:124071200-124083600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr12:124071200-124083800	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:124071200-124083800	Strong transcription	Placenta	Placenta
21	chr12:124071200-124084000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:124071200-124084000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr12:124071200-124084800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr12:124071400-124074600	Genic enhancers	Brain Germinal Matrix	brain
25	chr12:124071400-124077600	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr12:124071400-124082800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr12:124071400-124083000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:124071600-124084400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr12:124071800-124074600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:124071800-124083600	Strong transcription	Primary hematopoietic stem cells	blood
31	chr12:124072000-124076000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:124072200-124085800	Weak transcription	Small Intestine	intestine
33	chr12:124072400-124076800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:124072400-124077000	Strong transcription	Primary B cells from cord blood	blood
35	chr12:124072400-124077000	Strong transcription	HSMMtube	muscle
36	chr12:124072400-124082200	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr12:124072400-124083800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:124072600-124079200	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr12:124072600-124082400	Strong transcription	Thymus	Thymus
40	chr12:124072600-124083400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:124072600-124083400	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:124072800-124075800	Strong transcription	NHDF-Ad	bronchial
43	chr12:124072800-124077400	Strong transcription	Brain Anterior Caudate	brain
44	chr12:124072800-124077400	Strong transcription	HSMM	muscle
45	chr12:124072800-124084200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:124073000-124083600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr12:124073200-124075000	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr12:124073200-124075200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:124073200-124079400	Strong transcription	Fetal Intestine Small	intestine
50	chr12:124073200-124084200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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