Variant report

Variant	rs34743301
Chromosome Location	chr12:57559134-57559135
allele	G/T
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:5)
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	chr12:57558648-57560061	U87	brain:	n/a	n/a
2	POLR2A	chr12:57558334-57560061	U87	brain:	n/a	n/a
3	POLR2A	chr12:57558440-57559209	HepG2	liver:	n/a	n/a
4	RCOR1	chr12:57559022-57559196	K562	blood:	n/a	n/a
5	POLR2A	chr12:57557970-57562558	U87	brain:	n/a	n/a
6	POLR2A	chr12:57559006-57559152	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:57558312-57562558	U87	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:57558276..57561076-chr12:57569172..57570958,2	MCF-7	breast:
2	chr12:57520220..57523882-chr12:57558135..57563846,11	MCF-7	breast:
3	chr12:57480714..57483772-chr12:57558111..57562184,3	MCF-7	breast:
4	chr12:57520113..57524524-chr12:57557752..57564598,9	MCF-7	breast:
5	chr12:57529139..57531272-chr12:57558863..57560551,2	MCF-7	breast:

No data

Variant related genes	Relation type
LRP1	TF binding region
ENSG00000123384	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000166886	Chromatin interaction
ENSG00000166881	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs34293059	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34423990	0.89[ASN][1000 genomes]
rs34474417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34548137	0.89[ASN][1000 genomes]
rs34713147	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34736975	1.00[ASN][1000 genomes]
rs35425257	0.81[AFR][1000 genomes]
rs35792438	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35842116	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36049517	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv559023	chr12:57530670-57616061	Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv899112	chr12:57535266-57601388	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv525873	chr12:57535266-57616013	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv899113	chr12:57543572-57601388	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	12 gene(s)	inside rSNPs	diseases
7	nsv899114	chr12:57556768-57587839	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57531800-57576000	Strong transcription	Fetal Brain Female	brain
2	chr12:57540600-57569400	Strong transcription	Brain Germinal Matrix	brain
3	chr12:57541600-57560800	Strong transcription	Placenta Amnion	Placenta Amnion
4	chr12:57541600-57606600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:57541800-57607400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:57542200-57565600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:57546600-57565200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:57547000-57565200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:57547000-57575600	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr12:57547000-57575600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:57547000-57606400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:57547200-57562400	Weak transcription	Small Intestine	intestine
13	chr12:57547400-57567400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:57547400-57575400	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:57547600-57560600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:57547600-57575400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:57547600-57575600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:57547800-57565000	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr12:57547800-57565200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:57547800-57565400	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr12:57548000-57560400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:57548400-57561600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:57549000-57562400	Weak transcription	GM12878-XiMat	blood
24	chr12:57549000-57575200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:57552600-57563800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:57552600-57565000	Strong transcription	Fetal Stomach	stomach
27	chr12:57552800-57562400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:57552800-57563000	Strong transcription	Ovary	ovary
29	chr12:57552800-57564200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:57552800-57566800	Weak transcription	Right Atrium	heart
31	chr12:57552800-57568400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:57552800-57575200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr12:57552800-57606800	Strong transcription	Fetal Intestine Large	intestine
34	chr12:57552800-57607000	Strong transcription	Liver	Liver
35	chr12:57553000-57562600	Strong transcription	Brain Cingulate Gyrus	brain
36	chr12:57553000-57565000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:57553200-57607400	Strong transcription	Fetal Intestine Small	intestine
38	chr12:57553600-57564600	Strong transcription	Stomach Smooth Muscle	stomach
39	chr12:57553600-57565200	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr12:57553800-57563600	Strong transcription	Fetal Muscle Leg	muscle
41	chr12:57553800-57564600	Strong transcription	Colon Smooth Muscle	Colon
42	chr12:57554200-57563200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr12:57554400-57568800	Strong transcription	Brain Hippocampus Middle	brain
44	chr12:57555200-57560800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:57555400-57583200	Weak transcription	Fetal Heart	heart
46	chr12:57555800-57559600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:57556400-57559600	Weak transcription	Pancreas	Pancrea
48	chr12:57556800-57559400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr12:57556800-57559400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:57556800-57559600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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