Variant report

Variant	rs12424460
Chromosome Location	chr12:51495988-51495989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51474348..51478730-chr12:51495114..51501288,7	K562	blood:
2	chr12:51474877..51477433-chr12:51494301..51496579,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10876133	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs10876135	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs10876137	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876141	0.81[ASN][1000 genomes]
rs10876142	0.89[ASN][1000 genomes]
rs11169658	0.84[CHB][hapmap]
rs11169696	1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs11169700	0.90[ASN][1000 genomes]
rs11169706	1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs11169708	1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs11169720	0.90[ASN][1000 genomes]
rs11169721	0.88[ASN][1000 genomes]
rs11169722	0.90[ASN][1000 genomes]
rs11169734	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs11169735	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs11169737	0.85[ASN][1000 genomes]
rs11169747	0.86[JPT][hapmap]
rs11614806	0.83[ASN][1000 genomes]
rs12227032	0.90[ASN][1000 genomes]
rs12227973	0.91[ASN][1000 genomes]
rs12230388	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs12312531	0.99[ASN][1000 genomes]
rs1493382	0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs17125363	0.90[ASN][1000 genomes]
rs17125365	0.92[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs17125371	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2359189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2436636	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2452793	0.80[ASN][1000 genomes]
rs2452794	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2452795	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2452796	0.89[ASN][1000 genomes]
rs2640512	0.91[ASN][1000 genomes]
rs2640515	0.89[ASN][1000 genomes]
rs2640518	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs2640520	0.90[ASN][1000 genomes]
rs2640522	0.90[ASN][1000 genomes]
rs2640525	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2640526	0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2640528	0.91[ASN][1000 genomes]
rs2730651	0.85[ASN][1000 genomes]
rs2730653	0.90[ASN][1000 genomes]
rs2730657	0.92[ASN][1000 genomes]
rs2730659	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2934092	0.84[ASN][1000 genomes]
rs2956427	1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs2956433	0.83[ASN][1000 genomes]
rs4768953	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs4768957	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs4768971	0.89[ASN][1000 genomes]
rs4768974	0.90[ASN][1000 genomes]
rs56729853	0.91[ASN][1000 genomes]
rs60203224	0.82[ASN][1000 genomes]
rs7309374	0.89[ASN][1000 genomes]
rs7399208	0.83[ASN][1000 genomes]
rs7399214	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs7953765	0.99[ASN][1000 genomes]
rs7965004	0.82[ASN][1000 genomes]
rs7980076	0.85[ASN][1000 genomes]
rs8490	1.00[CHB][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51477400-51518200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51477800-51499600	Weak transcription	NHLF	lung
3	chr12:51477800-51518400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:51477800-51518400	Weak transcription	Pancreas	Pancrea
5	chr12:51477800-51550200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:51478000-51496000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:51482800-51498000	Strong transcription	Fetal Muscle Leg	muscle
8	chr12:51482800-51499400	Strong transcription	Fetal Stomach	stomach
9	chr12:51483800-51513400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:51484000-51502000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr12:51484000-51519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:51484400-51506000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:51484800-51507000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr12:51485000-51498400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:51485000-51507600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr12:51485000-51513200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:51485600-51498200	Strong transcription	Fetal Muscle Trunk	muscle
18	chr12:51485600-51498200	Strong transcription	Fetal Thymus	thymus
19	chr12:51485800-51497400	Strong transcription	Fetal Intestine Small	intestine
20	chr12:51485800-51513200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:51486000-51511400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:51486400-51510800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:51486600-51508000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:51486800-51497800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:51486800-51504600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:51486800-51508000	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr12:51487000-51498200	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:51487000-51505000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:51487000-51506600	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:51487000-51511400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr12:51487200-51498000	Strong transcription	Osteobl	bone
32	chr12:51487200-51498200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:51487200-51498400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:51487200-51502000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr12:51487200-51505000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:51487200-51508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr12:51487200-51513000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:51487200-51513200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:51487400-51496400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr12:51487400-51498200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr12:51487400-51511000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr12:51487600-51498000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr12:51487600-51498000	Strong transcription	Primary T cells from cord blood	blood
44	chr12:51487600-51498000	Strong transcription	Brain Anterior Caudate	brain
45	chr12:51487600-51498200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:51487600-51498400	Strong transcription	Primary B cells from peripheral blood	blood
47	chr12:51487600-51498400	Strong transcription	Placenta	Placenta
48	chr12:51487600-51504800	Strong transcription	Adipose Nuclei	Adipose
49	chr12:51487600-51508200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr12:51487600-51512000	Strong transcription	Primary T cells fromperipheralblood	blood

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