Variant report

Variant	rs12438453
Chromosome Location	chr15:42678609-42678610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42678390..42681163-chr15:42692112..42694875,2	K562	blood:

Variant related genes	Relation type
ENSG00000092529	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10775126	0.91[CEU][hapmap]
rs10851409	0.91[CEU][hapmap]
rs11070370	0.90[CEU][hapmap]
rs11631983	0.91[CEU][hapmap]
rs11638784	0.81[EUR][1000 genomes]
rs12438369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12438509	0.85[CHB][hapmap];0.87[YRI][hapmap]
rs12440087	0.85[CHB][hapmap]
rs12441642	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12441700	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs1359003	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs1359004	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs1659212	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs1678985	0.91[CEU][hapmap]
rs1678986	0.90[CEU][hapmap]
rs16972887	0.86[CHB][hapmap]
rs16973008	0.85[CHB][hapmap];0.91[YRI][hapmap]
rs16973045	0.86[CHB][hapmap]
rs16973060	0.86[CHB][hapmap]
rs1703750	0.91[CEU][hapmap]
rs1703755	0.82[CEU][hapmap]
rs1712418	0.91[CEU][hapmap]
rs2138831	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs2289295	0.91[CEU][hapmap]
rs2407707	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2412688	0.86[CHB][hapmap]
rs2412709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs28364388	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28364390	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28364393	0.85[CHB][hapmap];0.95[ASN][1000 genomes]
rs28364416	0.84[EUR][1000 genomes]
rs28745877	0.84[ASN][1000 genomes]
rs2918459	0.91[CEU][hapmap]
rs2918461	0.90[CEU][hapmap]
rs3743005	0.85[CHB][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs3743006	0.90[CEU][hapmap]
rs3743007	0.86[CHB][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs3743008	0.86[CHB][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs3825785	0.85[CHB][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs3850774	0.80[EUR][1000 genomes]
rs4329897	0.91[CEU][hapmap]
rs4506867	0.86[CHB][hapmap]
rs4923940	0.91[CEU][hapmap]
rs4923945	0.85[CHB][hapmap];0.88[YRI][hapmap]
rs4924630	0.86[CHB][hapmap]
rs4924645	0.91[CEU][hapmap]
rs4924653	0.88[CEU][hapmap]
rs4924658	0.90[CEU][hapmap]
rs4924672	0.85[CHB][hapmap];0.91[YRI][hapmap]
rs4924673	0.86[CHB][hapmap];0.88[YRI][hapmap]
rs4924674	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4924675	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs56702977	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57134130	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs57347762	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59094161	0.83[AFR][1000 genomes]
rs61133768	0.83[AFR][1000 genomes]
rs6493027	0.91[CEU][hapmap]
rs6493045	0.81[EUR][1000 genomes]
rs677878	0.89[CEU][hapmap]
rs7163986	0.91[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7166785	0.82[CEU][hapmap]
rs7168709	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7179203	0.87[AFR][1000 genomes]
rs7180279	0.85[CHB][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes]
rs7181742	0.90[CEU][hapmap]
rs7183015	0.90[CEU][hapmap]
rs7183546	0.90[CEU][hapmap]
rs73400993	0.84[ASN][1000 genomes]
rs73402707	0.81[AFR][1000 genomes]
rs751572	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8024113	0.82[CEU][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8024732	0.90[CEU][hapmap]
rs8025601	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8031315	0.90[CEU][hapmap]
rs8036187	1.00[CEU][hapmap]
rs8036596	0.90[CEU][hapmap]
rs8037020	0.90[CEU][hapmap]
rs9920921	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv832986	chr15:42587825-42753664	Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv832987	chr15:42627447-42792348	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv932995	chr15:42640015-42704121	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3334708	chr15:42664344-42827738	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42652800-42684400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr15:42653200-42691600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr15:42656000-42678800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:42656800-42693400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr15:42656800-42697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:42657200-42678800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr15:42663000-42691400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:42672400-42688800	Weak transcription	Esophagus	oesophagus
9	chr15:42673400-42691800	Weak transcription	Primary T cells from cord blood	blood
10	chr15:42674000-42694400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:42674600-42682600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr15:42674600-42684400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:42675200-42683600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr15:42675200-42684800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr15:42675200-42702800	Weak transcription	Colon Smooth Muscle	Colon
16	chr15:42675600-42691600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr15:42675800-42678800	Weak transcription	Brain Angular Gyrus	brain
18	chr15:42676200-42682400	Strong transcription	Liver	Liver
19	chr15:42676400-42679000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr15:42676400-42679200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr15:42676400-42679600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:42676400-42680600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:42676600-42679200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:42676600-42679800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr15:42676600-42680000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:42676600-42680200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:42676800-42679000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:42676800-42679200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:42676800-42679600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr15:42676800-42680200	Genic enhancers	Fetal Muscle Leg	muscle
31	chr15:42676800-42680400	Strong transcription	Primary B cells from cord blood	blood
32	chr15:42676800-42693200	Weak transcription	Fetal Stomach	stomach
33	chr15:42677000-42693400	Weak transcription	GM12878-XiMat	blood
34	chr15:42677200-42679200	Enhancers	Psoas Muscle	Psoas
35	chr15:42677200-42684000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr15:42677400-42680000	Genic enhancers	Adipose Nuclei	Adipose
37	chr15:42677400-42687800	Weak transcription	Brain Substantia Nigra	brain
38	chr15:42677600-42678800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:42677600-42679600	Enhancers	Fetal Muscle Trunk	muscle
40	chr15:42677600-42689000	Weak transcription	Right Ventricle	heart
41	chr15:42677800-42679000	Genic enhancers	Spleen	Spleen
42	chr15:42677800-42679200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:42677800-42679400	Enhancers	Fetal Thymus	thymus
44	chr15:42677800-42679600	Enhancers	K562	blood
45	chr15:42677800-42680200	Enhancers	HSMMtube	muscle
46	chr15:42677800-42682600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:42678000-42678800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr15:42678000-42678800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr15:42678000-42679200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
50	chr15:42678000-42679200	Enhancers	HUVEC	blood vessel

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