Variant report

Variant	rs824738
Chromosome Location	chr12:42540419-42540420
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42539891..42542441-chr12:42748681..42750572,2	MCF-7	breast:
2	chr12:42537957..42540928-chr12:42622624..42625244,2	MCF-7	breast:
3	chr12:42535865..42541158-chr12:42630084..42634162,10	K562	blood:
4	chr12:42536195..42540644-chr12:42629191..42634148,6	K562	blood:
5	chr12:42539265..42541316-chr12:42719076..42720974,2	K562	blood:
6	chr12:42537508..42540547-chr12:42555328..42558210,3	MCF-7	breast:
7	chr12:42537037..42538708-chr12:42539498..42541972,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139168	Chromatin interaction
ENSG00000151233	Chromatin interaction
ENSG00000015153	Chromatin interaction
ENSG00000134283	Chromatin interaction
ENSG00000269367	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1069644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10785335	0.84[ASN][1000 genomes]
rs10785337	0.80[ASN][1000 genomes]
rs10880275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10880279	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10880280	0.80[ASN][1000 genomes]
rs10880284	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs1118483	0.84[ASN][1000 genomes]
rs1226303	0.95[CEU][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1238290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12423383	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs1463613	0.95[CEU][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1628871	0.94[CEU][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1683198	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1683202	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1688854	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1688879	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1688884	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1732351	0.95[CEU][hapmap];0.87[JPT][hapmap]
rs1732352	0.95[CEU][hapmap];0.87[JPT][hapmap]
rs1826387	0.85[ASN][1000 genomes]
rs2061191	0.80[ASN][1000 genomes]
rs2061192	0.80[ASN][1000 genomes]
rs2100547	0.87[ASN][1000 genomes]
rs2198763	0.81[ASN][1000 genomes]
rs3761677	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs3827524	0.90[CHB][hapmap]
rs3852592	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4402364	0.84[ASN][1000 genomes]
rs4417370	0.84[ASN][1000 genomes]
rs4768397	0.91[CHB][hapmap]
rs4768398	0.92[CHB][hapmap];0.80[JPT][hapmap]
rs6582378	0.95[CEU][hapmap];0.87[JPT][hapmap]
rs6582389	0.82[ASN][1000 genomes]
rs6582392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs712106	0.95[CEU][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs712108	0.87[ASN][1000 genomes]
rs712109	0.84[ASN][1000 genomes]
rs712112	0.82[ASN][1000 genomes]
rs712114	0.87[ASN][1000 genomes]
rs712115	0.87[ASN][1000 genomes]
rs712118	0.83[ASN][1000 genomes]
rs712119	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs712120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs712122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs712123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs712125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs712129	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7298965	0.80[ASN][1000 genomes]
rs7302687	0.85[ASN][1000 genomes]
rs7303028	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7316575	0.85[ASN][1000 genomes]
rs7956016	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7959339	0.81[ASN][1000 genomes]
rs7960176	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7970115	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7978993	0.87[JPT][hapmap]
rs824697	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs824716	0.95[CEU][hapmap];0.87[JPT][hapmap]
rs824722	0.81[AMR][1000 genomes]
rs824724	0.95[CEU][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs824726	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs824734	0.95[CEU][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs824736	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs824739	0.89[ASN][1000 genomes]
rs824741	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs844046	0.95[CEU][hapmap];0.93[JPT][hapmap]
rs865420	0.95[CEU][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs866091	0.87[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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42539200-42552200	Weak transcription	HSMM	muscle
2	chr12:42539200-42563800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:42539400-42541000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:42539400-42551400	Weak transcription	Primary B cells from cord blood	blood
5	chr12:42539400-42551800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:42539400-42554000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:42539400-42554200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:42539400-42556000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr12:42539400-42577000	Weak transcription	Aorta	Aorta
10	chr12:42539400-42583200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:42539600-42540600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:42539600-42550200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:42539600-42550800	Weak transcription	Primary T cells from cord blood	blood
14	chr12:42539600-42550800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr12:42539600-42551600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:42539600-42551800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:42539600-42552200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:42539600-42552400	Weak transcription	HUVEC	blood vessel
19	chr12:42539600-42553600	Weak transcription	Adipose Nuclei	Adipose
20	chr12:42539600-42553800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:42539600-42553800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:42539600-42555800	Weak transcription	Brain Substantia Nigra	brain
23	chr12:42539600-42556200	Weak transcription	HSMMtube	muscle
24	chr12:42539600-42574000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:42539600-42578400	Weak transcription	Left Ventricle	heart
26	chr12:42539600-42586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:42539800-42541000	Enhancers	A549	lung
28	chr12:42539800-42550600	Weak transcription	Fetal Lung	lung
29	chr12:42539800-42550800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:42539800-42551600	Weak transcription	GM12878-XiMat	blood
31	chr12:42539800-42551800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr12:42539800-42551800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr12:42539800-42553000	Weak transcription	Hela-S3	cervix
34	chr12:42539800-42554200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr12:42539800-42568600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr12:42539800-42569000	Weak transcription	Fetal Kidney	kidney
37	chr12:42539800-42582800	Weak transcription	Spleen	Spleen
38	chr12:42539800-42607800	Weak transcription	Pancreas	Pancrea
39	chr12:42540000-42550600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:42540000-42552200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:42540000-42552200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:42540000-42553800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr12:42540000-42556000	Weak transcription	Fetal Intestine Small	intestine
44	chr12:42540000-42574800	Weak transcription	Brain Anterior Caudate	brain

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