Variant report

Variant	rs61942059
Chromosome Location	chr12:49107502-49107503
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49082621..49084947-chr12:49105438..49107834,2	K562	blood:
2	chr12:49105788..49107564-chr12:49110474..49111999,2	K562	blood:
3	chr12:49103301..49108658-chr12:49108679..49112078,7	K562	blood:
4	chr12:49106870..49108564-chr12:49207751..49210118,2	MCF-7	breast:
5	chr12:49072707..49077771-chr12:49103757..49111723,15	MCF-7	breast:
6	chr12:49075363..49077740-chr12:49105945..49108100,2	K562	blood:

Variant related genes	Relation type
ENSG00000167535	Chromatin interaction
ENSG00000129315	Chromatin interaction
ENSG00000139620	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10875851	1.00[ASN][1000 genomes]
rs11168620	1.00[ASN][1000 genomes]
rs11168659	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168660	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168661	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168664	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168667	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168680	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168690	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168691	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168692	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168699	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168700	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168701	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168708	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];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	1.00[ASN][1000 genomes]
rs11837643	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366919	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369279	1.00[ASN][1000 genomes]
rs17123362	1.00[ASN][1000 genomes]
rs17834622	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1895994	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2409084	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3013	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4132370	0.86[AMR][1000 genomes];0.90[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	0.86[EUR][1000 genomes]
rs61942012	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942013	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942014	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942015	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942016	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942018	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942047	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942048	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942049	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942051	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942052	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61942053	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61942058	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943193	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61943194	1.00[ASN][1000 genomes]
rs6580694	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138342	1.00[ASN][1000 genomes]
rs7294389	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295027	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295138	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296987	1.00[ASN][1000 genomes]
rs7303113	1.00[ASN][1000 genomes]
rs73105786	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74088163	1.00[ASN][1000 genomes]
rs7486636	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964801	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966343	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967175	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967542	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973954	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975102	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977935	1.00[ASN][1000 genomes]
rs7979508	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953673	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49076600-49109000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:49081600-49107600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:49081600-49108400	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:49082000-49107600	Strong transcription	Primary B cells from peripheral blood	blood
5	chr12:49082200-49108000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr12:49082200-49108400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr12:49082200-49108600	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:49082200-49108600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:49082200-49108800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:49082600-49107600	Strong transcription	Fetal Thymus	thymus
11	chr12:49088200-49107600	Weak transcription	Stomach Mucosa	stomach
12	chr12:49089800-49109400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:49090000-49107600	Weak transcription	Brain Angular Gyrus	brain
14	chr12:49090000-49107800	Weak transcription	Fetal Heart	heart
15	chr12:49090000-49108400	Weak transcription	Fetal Brain Male	brain
16	chr12:49093400-49108000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr12:49095000-49108600	Strong transcription	Fetal Stomach	stomach
18	chr12:49095600-49107800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:49095600-49108800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:49095800-49107600	Strong transcription	A549	lung
21	chr12:49095800-49108400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr12:49097600-49108600	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr12:49097600-49109400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:49097800-49108400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:49098200-49107600	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:49098200-49107800	Weak transcription	Fetal Kidney	kidney
27	chr12:49098200-49109600	Weak transcription	Aorta	Aorta
28	chr12:49098800-49108600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:49099200-49108600	Weak transcription	Gastric	stomach
30	chr12:49099200-49108800	Weak transcription	Brain Substantia Nigra	brain
31	chr12:49099400-49108400	Weak transcription	Right Ventricle	heart
32	chr12:49099600-49108000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:49099600-49108000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:49099600-49108200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:49099600-49109400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:49099800-49108600	Weak transcription	Esophagus	oesophagus
37	chr12:49100800-49107800	Strong transcription	Fetal Muscle Leg	muscle
38	chr12:49100800-49108200	Strong transcription	Fetal Intestine Small	intestine
39	chr12:49101000-49109000	Weak transcription	HSMMtube	muscle
40	chr12:49101600-49108400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:49102000-49107600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
42	chr12:49102800-49107600	Strong transcription	HUVEC	blood vessel
43	chr12:49103000-49108600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:49103200-49107800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:49103600-49108000	Strong transcription	Osteobl	bone
46	chr12:49103600-49108600	Genic enhancers	Primary T cells fromperipheralblood	blood
47	chr12:49103800-49107800	Weak transcription	Fetal Brain Female	brain
48	chr12:49103800-49108200	Strong transcription	Fetal Intestine Large	intestine
49	chr12:49104000-49108400	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr12:49104200-49107600	Strong transcription	Thymus	Thymus

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