Variant report

Variant	rs59601514
Chromosome Location	chr12:120603085-120603086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:120603051-120603431	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:120602075..120603746-chr12:120604439..120606392,2	K562	blood:
2	chr12:120554030..120557390-chr12:120602676..120607116,4	MCF-7	breast:
3	chr12:120601314..120603905-chr12:120622822..120624368,2	MCF-7	breast:
4	chr12:120577301..120580617-chr12:120600923..120603365,3	K562	blood:
5	chr12:120587276..120588807-chr12:120602039..120603973,2	K562	blood:

No data

Variant related genes	Relation type
GCN1L1	TF binding region
ENSG00000089154	Chromatin interaction
ENSG00000111737	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10437836	0.93[EUR][1000 genomes]
rs11065035	0.94[EUR][1000 genomes]
rs11065036	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11833158	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11836049	0.93[EUR][1000 genomes]
rs12305184	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12306075	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12310433	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12312562	0.94[EUR][1000 genomes]
rs12320253	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12578300	0.95[EUR][1000 genomes]
rs2074540	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2238155	0.90[EUR][1000 genomes]
rs2240314	0.83[EUR][1000 genomes]
rs2240315	0.90[EUR][1000 genomes]
rs2240317	0.94[EUR][1000 genomes]
rs2240318	0.96[EUR][1000 genomes]
rs2240319	0.96[EUR][1000 genomes]
rs2240320	0.95[EUR][1000 genomes]
rs2240321	0.96[EUR][1000 genomes]
rs2240322	0.96[EUR][1000 genomes]
rs2240323	0.95[EUR][1000 genomes]
rs2240325	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2269940	0.89[EUR][1000 genomes]
rs2269941	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2269943	0.88[EUR][1000 genomes]
rs2269944	0.96[EUR][1000 genomes]
rs2269945	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2283362	0.91[EUR][1000 genomes]
rs2286043	0.85[EUR][1000 genomes]
rs2286044	0.84[EUR][1000 genomes]
rs2286045	0.92[EUR][1000 genomes]
rs2286049	0.96[EUR][1000 genomes]
rs2286050	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2286051	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3742040	0.83[EUR][1000 genomes]
rs3815210	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4522230	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57546423	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57780521	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60271600	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7133235	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7134706	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7135914	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7294892	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7296380	0.87[ASN][1000 genomes]
rs7299429	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7301660	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7953741	0.83[EUR][1000 genomes]
rs7978061	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7978175	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9630281	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9651914	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][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	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription 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	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120563000-120605600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:120563000-120629800	Strong transcription	Fetal Stomach	stomach
3	chr12:120563000-120630200	Strong transcription	Fetal Muscle Leg	muscle
4	chr12:120563200-120630400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:120563400-120616200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:120563400-120629200	Strong transcription	Fetal Intestine Small	intestine
7	chr12:120563400-120630200	Strong transcription	Fetal Thymus	thymus
8	chr12:120563600-120603600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:120563600-120603800	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:120563600-120605600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:120563600-120626000	Strong transcription	Brain Cingulate Gyrus	brain
12	chr12:120563600-120626200	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr12:120563600-120629000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:120563600-120630200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:120563600-120630200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:120563600-120630200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr12:120563600-120630200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:120563600-120630200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr12:120563800-120603600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr12:120563800-120629800	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr12:120563800-120630000	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr12:120563800-120630200	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:120564000-120603600	Strong transcription	Brain Angular Gyrus	brain
24	chr12:120564000-120603800	Strong transcription	Thymus	Thymus
25	chr12:120564200-120624400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr12:120564200-120629600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr12:120564400-120603600	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:120564400-120603600	Strong transcription	Rectal Smooth Muscle	rectum
29	chr12:120564400-120603600	Strong transcription	Right Ventricle	heart
30	chr12:120564400-120628600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr12:120564400-120631800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr12:120564600-120603800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:120564600-120603800	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr12:120564800-120618000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:120565000-120603400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:120565000-120628800	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr12:120565000-120630200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:120565000-120630800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:120565200-120603600	Strong transcription	Spleen	Spleen
40	chr12:120565200-120603800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:120565200-120630200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:120565400-120618000	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr12:120565400-120628400	Strong transcription	Adipose Nuclei	Adipose
44	chr12:120565600-120603400	Strong transcription	Osteobl	bone
45	chr12:120565600-120603800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:120565600-120605000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:120565800-120625200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr12:120565800-120629400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:120565800-120630200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr12:120565800-120630400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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