Variant report

Variant	rs61942047
Chromosome Location	chr12:49052736-49052737
allele	A/G
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	chr12:49052676-49053199	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr12:49052653-49052880	MCF-7	breast:	n/a	n/a
3	POLR2A	chr12:49052468-49052771	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49052583..49059422-chr12:49071692..49076510,9	K562	blood:
2	chr12:49052650..49057544-chr12:49071692..49076123,6	K562	blood:

Variant related genes	Relation type
SNORA34	TF binding region
KANSL2	TF binding region
SNORA2A	TF binding region
ENSG00000139620	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10875851	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168620	1.00[ASN][1000 genomes]
rs11168659	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168660	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168661	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168664	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168680	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168690	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168691	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168692	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168693	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168694	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168695	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168699	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168700	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168701	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168708	1.00[ASN][1000 genomes]
rs11168715	1.00[ASN][1000 genomes]
rs11168717	1.00[ASN][1000 genomes]
rs11168718	1.00[ASN][1000 genomes]
rs11168719	1.00[ASN][1000 genomes]
rs11168722	1.00[ASN][1000 genomes]
rs11168727	1.00[ASN][1000 genomes]
rs11168781	1.00[ASN][1000 genomes]
rs11832160	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837643	1.00[ASN][1000 genomes]
rs12366919	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369279	1.00[ASN][1000 genomes]
rs17123362	1.00[ASN][1000 genomes]
rs17834622	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1895994	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409084	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3013	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4132370	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4405363	1.00[ASN][1000 genomes]
rs55644947	1.00[ASN][1000 genomes]
rs56182935	1.00[ASN][1000 genomes]
rs61942011	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61942012	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942013	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942015	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942016	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942018	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942048	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942049	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942051	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942052	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61942053	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61942058	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942059	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943193	1.00[ASN][1000 genomes]
rs61943194	1.00[ASN][1000 genomes]
rs6580694	1.00[ASN][1000 genomes]
rs7138342	1.00[ASN][1000 genomes]
rs7294389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295027	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295138	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296987	1.00[ASN][1000 genomes]
rs7303113	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73105786	1.00[ASN][1000 genomes]
rs74088163	1.00[ASN][1000 genomes]
rs7486636	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964801	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966343	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967175	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967542	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975102	1.00[ASN][1000 genomes]
rs7977935	1.00[ASN][1000 genomes]
rs7979508	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953673	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1043220	chr12:49045458-49065987	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1052256	chr12:49048506-49065987	Genic enhancers Strong transcription Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region	5 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	chr12:49036800-49072000	Strong transcription	Liver	Liver
2	chr12:49037800-49056600	Strong transcription	Fetal Muscle Trunk	muscle
3	chr12:49037800-49072400	Strong transcription	Placenta	Placenta
4	chr12:49038200-49070800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr12:49038400-49060600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:49038800-49071800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:49039000-49072200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:49039400-49068800	Weak transcription	Right Atrium	heart
9	chr12:49039400-49071800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:49039800-49071000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:49039800-49071000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr12:49040000-49057000	Strong transcription	Dnd41	blood
13	chr12:49040000-49059400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:49040000-49072600	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:49040400-49060600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:49040400-49072800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:49041000-49071800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:49041200-49061200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:49041200-49068200	Strong transcription	Stomach Smooth Muscle	stomach
20	chr12:49041600-49065200	Weak transcription	Stomach Mucosa	stomach
21	chr12:49041800-49054400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:49041800-49065200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:49041800-49070800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr12:49041800-49071000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr12:49041800-49072400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr12:49041800-49073800	Strong transcription	Fetal Intestine Large	intestine
27	chr12:49042400-49056800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:49042400-49065200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr12:49042400-49072800	Strong transcription	Fetal Muscle Leg	muscle
30	chr12:49042600-49064200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:49043600-49054600	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:49043800-49057600	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr12:49043800-49068800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:49044000-49055000	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:49044000-49068200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr12:49044200-49056600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:49044200-49057000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:49044200-49059800	Strong transcription	A549	lung
39	chr12:49044200-49071000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:49044200-49072400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:49044200-49072800	Strong transcription	Fetal Thymus	thymus
42	chr12:49044400-49056400	Strong transcription	Primary T cells from cord blood	blood
43	chr12:49044400-49056600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:49044400-49057000	Strong transcription	NHEK	skin
45	chr12:49044400-49065200	Strong transcription	Osteobl	bone
46	chr12:49044400-49071000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:49044400-49071400	Strong transcription	Thymus	Thymus
48	chr12:49044400-49072400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:49044600-49055400	Strong transcription	Brain Anterior Caudate	brain
50	chr12:49044600-49056600	Strong transcription	Adipose Nuclei	Adipose

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