Variant report

Variant	rs12066343
Chromosome Location	chr1:94050241-94050242
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93913254..93915566-chr1:94049347..94051024,2	MCF-7	breast:
2	chr1:94048697..94050277-chr1:94063385..94066022,2	MCF-7	breast:
3	chr1:94046974..94050616-chr1:94310637..94313716,4	MCF-7	breast:
4	chr1:94042226..94044912-chr1:94048849..94050610,3	MCF-7	breast:
5	chr1:94048472..94052407-chr1:94077212..94082015,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000211575	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000137942	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11576435	1.00[ASN][1000 genomes]
rs11577352	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579004	1.00[ASN][1000 genomes]
rs11579685	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580965	1.00[ASN][1000 genomes]
rs11588860	1.00[ASN][1000 genomes]
rs12073093	1.00[ASN][1000 genomes]
rs12090736	1.00[ASN][1000 genomes]
rs12732557	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739747	1.00[ASN][1000 genomes]
rs12740779	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12744941	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757325	1.00[ASN][1000 genomes]
rs12760092	1.00[ASN][1000 genomes]
rs17110063	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110101	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110111	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110225	1.00[ASN][1000 genomes]
rs17110370	1.00[ASN][1000 genomes]
rs1877603	1.00[ASN][1000 genomes]
rs1877604	1.00[ASN][1000 genomes]
rs1891138	1.00[ASN][1000 genomes]
rs2818163	1.00[ASN][1000 genomes]
rs34183660	1.00[ASN][1000 genomes]
rs34423897	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34663884	1.00[ASN][1000 genomes]
rs34666525	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34726063	1.00[ASN][1000 genomes]
rs35126293	1.00[ASN][1000 genomes]
rs35691338	1.00[ASN][1000 genomes]
rs35896714	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35972761	1.00[ASN][1000 genomes]
rs36115605	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3950119	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59996315	1.00[ASN][1000 genomes]
rs61780979	1.00[ASN][1000 genomes]
rs61780999	1.00[ASN][1000 genomes]
rs6660968	1.00[ASN][1000 genomes]
rs6666778	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677770	1.00[ASN][1000 genomes]
rs6679609	1.00[ASN][1000 genomes]
rs6683296	1.00[ASN][1000 genomes]
rs66966060	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67043929	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67300695	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67354439	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67511232	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71652539	1.00[ASN][1000 genomes]
rs72721041	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7511890	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514579	0.83[EUR][1000 genomes]
rs7525880	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531106	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543098	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543734	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7543763	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553185	1.00[ASN][1000 genomes]
rs7555302	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761802	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];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	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94020800-94050600	Weak transcription	Fetal Thymus	thymus
2	chr1:94025600-94073800	Weak transcription	Fetal Brain Female	brain
3	chr1:94031800-94052400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:94032000-94053600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr1:94038400-94054000	Weak transcription	Brain Substantia Nigra	brain
6	chr1:94038400-94054800	Weak transcription	Brain Angular Gyrus	brain
7	chr1:94038600-94051800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:94038600-94054200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:94040000-94055000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:94041800-94059400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:94042000-94054800	Weak transcription	Primary B cells from cord blood	blood
12	chr1:94042200-94063200	Weak transcription	Brain Germinal Matrix	brain
13	chr1:94042800-94050600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:94042800-94053000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:94043000-94058400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:94043200-94050400	Strong transcription	NHEK	skin
17	chr1:94045000-94050400	Genic enhancers	A549	lung
18	chr1:94045400-94053600	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:94046000-94050600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:94046000-94051600	Strong transcription	NH-A	brain
21	chr1:94046400-94050400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:94046600-94058200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:94047000-94051200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:94047200-94051000	Genic enhancers	Fetal Muscle Trunk	muscle
25	chr1:94047200-94053600	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr1:94047400-94050800	Strong transcription	Primary B cells from peripheral blood	blood
27	chr1:94047400-94051200	Genic enhancers	Fetal Muscle Leg	muscle
28	chr1:94047400-94053400	Strong transcription	HUVEC	blood vessel
29	chr1:94047600-94050400	Strong transcription	Brain Anterior Caudate	brain
30	chr1:94047600-94050600	Active TSS	Stomach Mucosa	stomach
31	chr1:94047600-94050800	Strong transcription	Spleen	Spleen
32	chr1:94047600-94051400	Genic enhancers	Placenta	Placenta
33	chr1:94048000-94050600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:94048200-94052000	Weak transcription	Fetal Lung	lung
35	chr1:94048200-94054600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:94048200-94059200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:94048200-94059400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:94048400-94051000	Active TSS	Colonic Mucosa	Colon
39	chr1:94048400-94053200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:94048400-94059600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:94048600-94064200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:94048800-94052200	Genic enhancers	NHDF-Ad	bronchial
43	chr1:94048800-94053800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:94049000-94051800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:94049000-94052000	Genic enhancers	Adipose Nuclei	Adipose
46	chr1:94049400-94050600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:94049400-94051400	Genic enhancers	HSMM	muscle
48	chr1:94049400-94051800	Genic enhancers	Osteobl	bone
49	chr1:94049400-94052200	Genic enhancers	Hela-S3	cervix
50	chr1:94049600-94050600	Weak transcription	Ovary	ovary

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