Variant report

Variant	rs998225
Chromosome Location	chr15:72757197-72757198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:72750881..72760234-chr15:72764528..72769120,23	MCF-7	breast:
2	chr15:72750207..72758265-chr15:72764578..72767350,10	MCF-7	breast:
3	chr15:72667186..72669551-chr15:72756873..72758557,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HEXA-3	chr15:72757151-72757459	XLOC_011523
2	lnc-HEXA-3	chr15:72757151-72757459	XLOC_011523

Variant related genes	Relation type
ENSG00000260339	Chromatin interaction
ENSG00000213614	Chromatin interaction
ENSG00000261423	Chromatin interaction
ENSG00000260729	Chromatin interaction
ENSG00000166233	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10152810	0.81[MEX][hapmap]
rs10220917	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11072372	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12324592	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12439127	1.00[ASN][1000 genomes]
rs12903882	1.00[ASN][1000 genomes]
rs13379855	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16953788	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16956667	1.00[ASN][1000 genomes]
rs16956675	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16956759	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16956826	1.00[CHB][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16956904	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs16956917	0.81[MEX][hapmap]
rs16957154	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16957161	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16957189	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1816645	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1963894	1.00[ASN][1000 genomes]
rs28393893	1.00[ASN][1000 genomes]
rs28408413	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28422889	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28435710	1.00[ASN][1000 genomes]
rs28437631	1.00[EUR][1000 genomes]
rs28439115	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28453701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28471053	1.00[ASN][1000 genomes]
rs28488862	1.00[ASN][1000 genomes]
rs28493570	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28534054	1.00[ASN][1000 genomes]
rs28541481	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28602765	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661594	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28795465	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28832330	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28853391	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2912208	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2912209	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2912211	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2912212	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2912213	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2959936	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2959942	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35293819	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4556749	0.81[MEX][hapmap]
rs4777516	1.00[ASN][1000 genomes]
rs6495002	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs72735194	1.00[ASN][1000 genomes]
rs73440555	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73440562	1.00[ASN][1000 genomes]
rs73440566	1.00[ASN][1000 genomes]
rs73440586	1.00[ASN][1000 genomes]
rs73442510	1.00[ASN][1000 genomes]
rs8039489	1.00[ASN][1000 genomes]
rs8192349	1.00[ASN][1000 genomes]
rs9806212	1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9806258	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9806374	1.00[CHB][hapmap];0.89[MEX][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9944261	1.00[ASW][hapmap];1.00[CHB][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
3	nsv534037	chr15:72659210-72964029	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer 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	nsv469704	chr15:72669374-72853927	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
5	nsv482685	chr15:72669374-72853927	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	50 gene(s)	inside rSNPs	diseases
6	nsv1050558	chr15:72739150-72860350	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
7	nsv542427	chr15:72739150-72860350	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72754600-72764800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:72754600-72765400	Weak transcription	NHDF-Ad	bronchial
3	chr15:72754800-72765000	Weak transcription	Primary T cells from cord blood	blood
4	chr15:72754800-72765000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr15:72754800-72765200	Weak transcription	Brain Angular Gyrus	brain
6	chr15:72754800-72765200	Weak transcription	Brain Substantia Nigra	brain
7	chr15:72754800-72765400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr15:72754800-72765400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:72754800-72765400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:72754800-72765400	Weak transcription	Colon Smooth Muscle	Colon
11	chr15:72754800-72765400	Weak transcription	Fetal Lung	lung
12	chr15:72754800-72765400	Weak transcription	Placenta	Placenta
13	chr15:72754800-72765400	Weak transcription	Lung	lung
14	chr15:72754800-72765400	Weak transcription	Right Ventricle	heart
15	chr15:72754800-72765400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:72754800-72765600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr15:72755000-72758000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:72755000-72758200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr15:72755000-72763200	Weak transcription	Brain Anterior Caudate	brain
20	chr15:72755000-72763600	Weak transcription	Liver	Liver
21	chr15:72755000-72763600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:72755000-72763600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr15:72755000-72764600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:72755000-72764600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr15:72755000-72765000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr15:72755000-72765000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr15:72755000-72765000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr15:72755000-72765000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr15:72755000-72765000	Weak transcription	NHLF	lung
30	chr15:72755000-72765200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:72755000-72765200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:72755000-72765200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr15:72755000-72765200	Weak transcription	HSMM	muscle
34	chr15:72755000-72765400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:72755000-72765400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr15:72755000-72765400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:72755000-72765400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr15:72755000-72765400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:72755000-72765600	Weak transcription	Left Ventricle	heart
40	chr15:72755000-72766000	Weak transcription	Ovary	ovary
41	chr15:72755800-72765000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr15:72756000-72759400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:72756400-72757200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:72756400-72757400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr15:72756400-72763200	Weak transcription	Brain Hippocampus Middle	brain
46	chr15:72756800-72757400	Enhancers	GM12878-XiMat	blood
47	chr15:72757000-72757400	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr15:72757000-72765000	Weak transcription	Adipose Nuclei	Adipose
49	chr15:72757000-72765200	Weak transcription	Primary B cells from peripheral blood	blood

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