Variant report

Variant	rs2280574
Chromosome Location	chr12:122492978-122492979
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122492842..122494404-chr12:122622971..122625233,2	K562	blood:
2	chr12:122491384..122494042-chr12:122494209..122496970,2	MCF-7	breast:
3	chr12:122491823..122494895-chr12:122496656..122499239,3	K562	blood:
4	chr12:122491890..122493016-chr12:122610733..122612779,17	MCF-7	breast:
5	chr12:122491108..122493990-chr12:122605278..122608052,2	K562	blood:
6	chr12:122492378..122493010-chr12:122636236..122636816,2	K562	blood:
7	chr12:122492400..122494869-chr12:122515586..122517773,2	K562	blood:
8	chr12:122491967..122493498-chr12:122607388..122608388,14	K562	blood:
9	chr12:122491216..122493323-chr12:122496696..122498393,2	K562	blood:
10	chr12:122492460..122495753-chr12:122599733..122603330,4	MCF-7	breast:
11	chr12:122492379..122495152-chr12:122604029..122610434,5	MCF-7	breast:
12	chr12:122491907..122493455-chr12:122607305..122608643,21	MCF-7	breast:
13	chr12:122492846..122494927-chr12:122498061..122499591,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000175727	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10770189	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10773037	0.83[EUR][1000 genomes]
rs10840645	0.92[ASN][1000 genomes]
rs11057184	0.83[EUR][1000 genomes]
rs11057654	0.82[EUR][1000 genomes]
rs11059094	0.89[CEU][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs11060477	0.83[EUR][1000 genomes]
rs11608788	0.83[EUR][1000 genomes]
rs11608792	0.83[EUR][1000 genomes]
rs11609875	0.82[EUR][1000 genomes]
rs11835818	0.92[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12230227	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12366611	0.83[EUR][1000 genomes]
rs12812519	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1316787	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1880030	0.94[ASN][1000 genomes]
rs1976859	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2280573	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28385906	0.82[EUR][1000 genomes]
rs28401575	0.83[EUR][1000 genomes]
rs28414202	0.83[EUR][1000 genomes]
rs28421373	0.82[EUR][1000 genomes]
rs28430881	0.83[EUR][1000 genomes]
rs28450064	0.82[EUR][1000 genomes]
rs28453771	0.80[EUR][1000 genomes]
rs28461580	0.89[CEU][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs28464252	0.83[EUR][1000 genomes]
rs28478366	0.83[EUR][1000 genomes]
rs28478717	0.83[EUR][1000 genomes]
rs28498002	0.83[EUR][1000 genomes]
rs28498376	0.83[EUR][1000 genomes]
rs28503672	0.83[EUR][1000 genomes]
rs28506952	0.82[EUR][1000 genomes]
rs28517281	0.83[EUR][1000 genomes]
rs28529535	0.83[EUR][1000 genomes]
rs28530689	0.87[EUR][1000 genomes]
rs28548845	0.83[EUR][1000 genomes]
rs28569273	0.82[EUR][1000 genomes]
rs28585613	0.82[EUR][1000 genomes]
rs28591322	0.83[EUR][1000 genomes]
rs28605425	0.89[CEU][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs28607028	0.83[EUR][1000 genomes]
rs28626850	0.83[EUR][1000 genomes]
rs28629903	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28631172	0.81[EUR][1000 genomes]
rs28639626	0.83[EUR][1000 genomes]
rs28649184	0.83[EUR][1000 genomes]
rs28652632	0.89[CEU][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs28683032	0.83[EUR][1000 genomes]
rs28691281	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28699616	0.83[EUR][1000 genomes]
rs28737311	0.83[EUR][1000 genomes]
rs28739522	0.83[EUR][1000 genomes]
rs28759327	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34047484	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34123446	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34532891	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34739240	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34741056	0.81[EUR][1000 genomes]
rs34974633	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35159488	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35249105	0.87[EUR][1000 genomes]
rs35676267	0.85[EUR][1000 genomes]
rs35764187	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36079122	0.84[EUR][1000 genomes]
rs4758690	0.89[CEU][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]
rs61952902	0.87[EUR][1000 genomes]
rs61952904	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61952920	0.83[EUR][1000 genomes]
rs61952922	0.84[EUR][1000 genomes]
rs61952923	0.82[EUR][1000 genomes]
rs7137049	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7299842	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7485447	0.89[CEU][hapmap];0.84[GIH][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv899569	chr12:122478728-122630909	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv527450	chr12:122481290-122676531	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2280574	FAM101A	cis	cerebellum	SCAN
rs2280574	CCDC92	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122462400-122500000	Weak transcription	Hela-S3	cervix
2	chr12:122466200-122500800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr12:122467800-122500000	Strong transcription	Thymus	Thymus
4	chr12:122467800-122500200	Strong transcription	Dnd41	blood
5	chr12:122472000-122507200	Weak transcription	Fetal Brain Male	brain
6	chr12:122474000-122496800	Weak transcription	HMEC	breast
7	chr12:122474400-122496600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:122474400-122500600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:122475200-122501400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:122479200-122493200	Weak transcription	Gastric	stomach
11	chr12:122479400-122500600	Weak transcription	Small Intestine	intestine
12	chr12:122483600-122500200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:122484600-122493000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:122484800-122493000	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:122484800-122495200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:122485000-122494200	Weak transcription	Brain Angular Gyrus	brain
17	chr12:122488000-122493400	Weak transcription	Fetal Kidney	kidney
18	chr12:122488000-122500600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr12:122488600-122493000	Weak transcription	Primary B cells from cord blood	blood
20	chr12:122488800-122493000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:122489400-122493000	Weak transcription	Aorta	Aorta
22	chr12:122489400-122494200	Weak transcription	Spleen	Spleen
23	chr12:122489400-122495000	Weak transcription	NHLF	lung
24	chr12:122489400-122498000	Weak transcription	Right Atrium	heart
25	chr12:122489600-122493000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:122489600-122493000	Weak transcription	Brain Germinal Matrix	brain
27	chr12:122489600-122493000	Weak transcription	Lung	lung
28	chr12:122489600-122493800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr12:122489600-122499800	Weak transcription	HUVEC	blood vessel
30	chr12:122490400-122494200	Weak transcription	HSMMtube	muscle
31	chr12:122491200-122500000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:122491800-122501000	Strong transcription	Fetal Brain Female	brain
33	chr12:122492000-122493200	Enhancers	Liver	Liver
34	chr12:122492200-122493000	Enhancers	Stomach Mucosa	stomach
35	chr12:122492200-122493000	Enhancers	HepG2	liver
36	chr12:122492200-122493200	Genic enhancers	Fetal Muscle Trunk	muscle
37	chr12:122492200-122493200	Genic enhancers	Fetal Muscle Leg	muscle
38	chr12:122492200-122493200	Genic enhancers	Fetal Stomach	stomach
39	chr12:122492200-122493200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr12:122492200-122495600	Genic enhancers	Fetal Intestine Small	intestine
41	chr12:122492400-122493000	Enhancers	Colonic Mucosa	Colon
42	chr12:122492400-122493000	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr12:122492400-122493200	Genic enhancers	A549	lung
44	chr12:122492400-122493400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:122492400-122493400	Genic enhancers	Pancreas	Pancrea
46	chr12:122492400-122495800	Genic enhancers	Fetal Intestine Large	intestine
47	chr12:122492400-122497400	Strong transcription	K562	blood
48	chr12:122492400-122499400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr12:122492400-122500200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:122492400-122500400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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