Variant report

Variant	rs12296189
Chromosome Location	chr12:49578118-49578119
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr12:49576977-49578130	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr12:49575803-49578313	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr12:49577036-49578226	H1-neurons	neurons:	n/a	n/a
4	REST	chr12:49575982-49579090	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr12:49577327-49578123	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr12:49576928-49578792	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr12:49577415-49578180	A549	lung:	n/a	n/a
8	POLR2A	chr12:49577057-49578156	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr12:49576930-49578155	HUVEC	blood vessel:	n/a	n/a
10	JUND	chr12:49577260-49578171	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr12:49577761-49578204	HL-60	blood:	n/a	n/a
12	POLR2A	chr12:49577395-49578149	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr12:49576836-49579887	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr12:49577041-49578970	IMR90	lung:	n/a	n/a
15	POLR2A	chr12:49577076-49578294	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr12:49577493-49578138	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr12:49576997-49579245	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr12:49577328-49578327	SK-N-SH	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49521045..49522741-chr12:49576322..49578574,2	K562	blood:
2	chr12:49455381..49457675-chr12:49576315..49579055,2	MCF-7	breast:
3	chr12:49523810..49525846-chr12:49575368..49579813,5	K562	blood:
4	chr12:49577117..49578684-chr12:49582643..49584249,2	K562	blood:

No data

Variant related genes	Relation type
TUBA1C	TF binding region
ENSG00000123416	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000167552	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10219709	1.00[AMR][1000 genomes]
rs11168898	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168899	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168913	1.00[AMR][1000 genomes]
rs11168916	1.00[AMR][1000 genomes]
rs11168918	1.00[AMR][1000 genomes]
rs11168923	1.00[AMR][1000 genomes]
rs12296265	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12297125	0.83[AMR][1000 genomes]
rs12298540	0.91[AFR][1000 genomes]
rs12298869	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12307514	0.83[AMR][1000 genomes]
rs12308383	0.91[AFR][1000 genomes]
rs12315823	1.00[AMR][1000 genomes]
rs12318970	1.00[AMR][1000 genomes]
rs12321120	1.00[AMR][1000 genomes]
rs12322965	1.00[AMR][1000 genomes]
rs61648563	1.00[AFR][1000 genomes];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	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	esv3417605	chr12:49521878-49578961	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
5	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
6	nsv976610	chr12:49577937-49580571	Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49570600-49581000	Weak transcription	GM12878-XiMat	blood
2	chr12:49570800-49578400	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:49574200-49578600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:49574200-49580600	Weak transcription	Primary B cells from cord blood	blood
5	chr12:49575000-49578400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:49575200-49578200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:49575200-49578800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:49575800-49578200	Weak transcription	Fetal Lung	lung
9	chr12:49576000-49578200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:49576000-49578200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:49576000-49578200	Weak transcription	Fetal Intestine Large	intestine
12	chr12:49576000-49578600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:49576000-49580800	Weak transcription	A549	lung
14	chr12:49576200-49578200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:49576200-49578600	Weak transcription	Placenta	Placenta
16	chr12:49576200-49579200	Weak transcription	Fetal Intestine Small	intestine
17	chr12:49576200-49580800	Weak transcription	Fetal Kidney	kidney
18	chr12:49576400-49578200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:49576400-49578200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:49576400-49578400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:49576400-49578600	Weak transcription	Aorta	Aorta
22	chr12:49576400-49578800	Weak transcription	Brain Substantia Nigra	brain
23	chr12:49576400-49578800	Weak transcription	Colon Smooth Muscle	Colon
24	chr12:49576400-49580000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:49576600-49578200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:49576600-49578200	Weak transcription	Spleen	Spleen
27	chr12:49576600-49578800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:49576800-49578400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr12:49576800-49578400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:49576800-49578400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:49576800-49578400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:49576800-49578400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:49576800-49578400	Weak transcription	Dnd41	blood
34	chr12:49576800-49581800	Weak transcription	Liver	Liver
35	chr12:49577000-49578600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:49577000-49578600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr12:49577000-49579200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:49577000-49579400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:49577000-49580200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:49577000-49581600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr12:49577200-49578400	Weak transcription	HUVEC	blood vessel
42	chr12:49577200-49578600	Genic enhancers	Brain Anterior Caudate	brain
43	chr12:49577200-49578800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr12:49577200-49578800	Weak transcription	Ovary	ovary
45	chr12:49577200-49578800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:49577200-49580200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:49577200-49580800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr12:49577200-49581000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:49577200-49581000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr12:49577400-49578600	Genic enhancers	Brain Hippocampus Middle	brain

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