Variant report

Variant	rs1800194
Chromosome Location	chr12:57567762-57567763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57518177..57519881-chr12:57566429..57568200,2	MCF-7	breast:
2	chr12:57562872..57564525-chr12:57565091..57567935,2	MCF-7	breast:
3	chr12:57567624..57569926-chr12:57631899..57633807,2	K562	blood:
4	chr12:57479971..57483845-chr12:57566210..57569017,3	K562	blood:
5	chr12:57517554..57518923-chr12:57566402..57567852,18	MCF-7	breast:
6	chr12:57567688..57569393-chr12:57569418..57572218,2	K562	blood:
7	chr12:57520537..57522971-chr12:57567650..57571522,4	MCF-7	breast:
8	chr12:57559440..57562772-chr12:57563744..57569103,7	MCF-7	breast:
9	chr12:57567760..57571658-chr12:57632861..57635535,3	K562	blood:
10	chr12:57564778..57567852-chr12:57580011..57582534,3	K562	blood:
11	chr12:57517817..57518701-chr12:57566698..57567928,6	MCF-7	breast:
12	chr12:57564778..57568502-chr12:57580650..57583598,4	K562	blood:
13	chr12:57547530..57549033-chr12:57566577..57569011,2	K562	blood:
14	chr12:57561115..57562927-chr12:57565880..57567819,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000166888	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000123384	Chromatin interaction
ENSG00000185633	Chromatin interaction
ENSG00000166886	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10876967	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172122	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1140648	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11837145	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1800139	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1800154	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1800156	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1800165	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1800166	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1800168	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1800174	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800175	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800176	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1800177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800180	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800181	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1800182	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1800187	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1800189	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1800191	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4074308	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4074309	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4077658	0.80[EUR][1000 genomes]
rs6581125	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6581128	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7305179	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7312323	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7398391	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7398426	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7975818	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' 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:96 , 50 per page) page: 1 2

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	chr12:57541600-57606600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:57541800-57607400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:57547000-57575600	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr12:57547000-57575600	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:57547000-57606400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:57547400-57575400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:57547600-57575400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:57547600-57575600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:57549000-57575200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:57552800-57568400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:57552800-57575200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr12:57552800-57606800	Strong transcription	Fetal Intestine Large	intestine
15	chr12:57552800-57607000	Strong transcription	Liver	Liver
16	chr12:57553200-57607400	Strong transcription	Fetal Intestine Small	intestine
17	chr12:57554400-57568800	Strong transcription	Brain Hippocampus Middle	brain
18	chr12:57555400-57583200	Weak transcription	Fetal Heart	heart
19	chr12:57557400-57606800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr12:57558000-57575800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:57558400-57568200	Strong transcription	Rectal Smooth Muscle	rectum
22	chr12:57558400-57575600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr12:57558600-57568200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr12:57558800-57575600	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:57560800-57606200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:57560800-57606600	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr12:57561400-57567800	Strong transcription	NH-A	brain
28	chr12:57561800-57568400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:57562000-57569200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:57562000-57570800	Weak transcription	Pancreas	Pancrea
31	chr12:57562200-57569200	Weak transcription	A549	lung
32	chr12:57563000-57568400	Weak transcription	Fetal Thymus	thymus
33	chr12:57563000-57569200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:57563400-57569200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:57563600-57573800	Weak transcription	Small Intestine	intestine
36	chr12:57563800-57569200	Strong transcription	Brain Anterior Caudate	brain
37	chr12:57564000-57572200	Weak transcription	Left Ventricle	heart
38	chr12:57564600-57568200	Genic enhancers	Esophagus	oesophagus
39	chr12:57564600-57570000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:57565400-57570000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:57565400-57574400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr12:57565400-57575600	Strong transcription	Lung	lung
43	chr12:57565600-57569200	Strong transcription	HSMM	muscle
44	chr12:57565600-57569400	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr12:57565600-57573800	Strong transcription	Adipose Nuclei	Adipose
46	chr12:57565600-57576200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:57565800-57568400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:57565800-57568800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr12:57565800-57569200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:57565800-57569200	Strong transcription	Placenta	Placenta

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