Variant report

Variant	rs12911999
Chromosome Location	chr15:39977641-39977642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:39879533..39881128-chr15:39975849..39978589,2	MCF-7	breast:
2	chr15:39970946..39972783-chr15:39976186..39977886,2	MCF-7	breast:
3	chr15:39977207..39979159-chr15:39990602..39992278,2	K562	blood:
4	chr15:39976358..39978991-chr15:39987825..39990232,2	K562	blood:

Variant related genes	Relation type
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1105159	0.95[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs11070231	0.90[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs11631820	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11631824	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12050804	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12899323	0.86[ASN][1000 genomes]
rs12900024	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12900583	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12901142	0.89[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs12903514	0.87[ASN][1000 genomes]
rs12911549	0.95[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs1906152	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1906155	0.91[ASN][1000 genomes]
rs1906156	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1994379	0.90[CHB][hapmap]
rs2129459	0.92[ASN][1000 genomes]
rs2411299	0.89[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs2411300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2411301	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2411304	0.81[ASN][1000 genomes]
rs2411307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2411308	0.86[ASN][1000 genomes]
rs2411309	0.89[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs2411310	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2411311	0.90[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2631697	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2631700	0.95[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2631701	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2631702	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[ASN][1000 genomes]
rs2631704	0.97[ASN][1000 genomes]
rs2631705	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[ASN][1000 genomes]
rs2631710	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2664125	0.97[ASN][1000 genomes]
rs2664133	0.92[ASN][1000 genomes]
rs2664135	0.90[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap];0.93[ASN][1000 genomes]
rs28437905	0.87[ASN][1000 genomes]
rs28581473	0.91[ASN][1000 genomes]
rs2898685	0.90[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs3103065	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4319738	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4429263	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4476148	0.98[ASN][1000 genomes]
rs4480779	0.95[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4493017	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4505280	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4572354	0.89[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs4591113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4606692	0.90[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4924376	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4924377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6492909	0.89[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs6492910	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6492911	0.95[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs68183224	0.93[ASN][1000 genomes]
rs7167100	0.87[ASN][1000 genomes]
rs7177857	0.92[ASN][1000 genomes]
rs7179013	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs8033902	0.89[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs8034543	0.92[ASN][1000 genomes]
rs8034885	0.86[ASN][1000 genomes]
rs8035354	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8036226	0.87[ASN][1000 genomes]
rs8042068	0.86[ASN][1000 genomes]
rs937960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs951358	0.90[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs9672572	0.89[ASN][1000 genomes]

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	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39972600-39978800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr15:39973400-39982800	Weak transcription	Fetal Lung	lung
3	chr15:39973800-39982800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:39974200-39978400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:39974800-39985000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:39975000-39978000	Weak transcription	HSMM	muscle
7	chr15:39975000-39978600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:39975400-39982000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:39975400-39984400	Weak transcription	Fetal Kidney	kidney
10	chr15:39975600-39978000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:39976800-39978000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:39976800-39978400	Enhancers	Osteobl	bone
13	chr15:39976800-39978800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:39977000-39978200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:39977000-39978200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:39977000-39978400	Enhancers	HSMMtube	muscle
17	chr15:39977200-39990600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:39977600-39978200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:39977600-39978600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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