Variant report

Variant	rs62023641
Chromosome Location	chr15:99678877-99678878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:99678809-99679690	Hela-S3	cervix:	n/a	n/a
2	FOSL2	chr15:99678642-99679039	HepG2	liver:	n/a	n/a
3	POLR2A	chr15:99678673-99679259	A549	lung:	n/a	n/a
4	MYC	chr15:99678877-99679008	MCF-7	breast:	n/a	n/a
5	POLR2A	chr15:99678816-99678964	A549	lung:	n/a	n/a
6	POLR2A	chr15:99678794-99679178	A549	lung:	n/a	n/a
7	POLR2A	chr15:99678838-99679288	PANC-1	pancreas:	n/a	n/a
8	CTCF	chr15:99678860-99679010	HEK293	kidney:	n/a	n/a
9	CTCF	chr15:99678840-99678990	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99676254..99679133-chr15:99680530..99682428,2	K562	blood:
2	chr15:99677279..99681777-chr15:99693510..99696751,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261616	TF binding region
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10444900	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10444901	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13853	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466191	0.91[EUR][1000 genomes]
rs1670238	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1670247	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1703775	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1703781	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1703783	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs260086	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2654965	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28617660	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28690249	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5030691	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62023639	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62023640	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023643	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62025375	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7170268	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7176156	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7176176	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8031137	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038315	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038677	0.96[ASN][1000 genomes]
rs8041090	0.83[EUR][1000 genomes]
rs8043501	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv533375	chr15:99443534-99696221	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
16	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99663600-99679400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:99664600-99682200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:99664800-99682000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:99664800-99688600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:99665000-99683800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr15:99665000-99714200	Weak transcription	NHEK	skin
7	chr15:99665200-99679400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:99665200-99687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:99666000-99683000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:99666200-99680400	Weak transcription	Fetal Brain Female	brain
11	chr15:99666200-99684200	Weak transcription	HSMMtube	muscle
12	chr15:99666400-99679800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
13	chr15:99667600-99679200	Strong transcription	Fetal Muscle Leg	muscle
14	chr15:99669000-99679400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr15:99670800-99680600	Weak transcription	Thymus	Thymus
16	chr15:99671800-99679200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr15:99673000-99679400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
19	chr15:99673400-99679800	Genic enhancers	Stomach Smooth Muscle	stomach
20	chr15:99674400-99704200	Weak transcription	Fetal Kidney	kidney
21	chr15:99674600-99679800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr15:99676000-99679000	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:99676000-99679800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:99676000-99679800	Strong transcription	Fetal Intestine Large	intestine
25	chr15:99676000-99683200	Weak transcription	Stomach Mucosa	stomach
26	chr15:99676200-99679000	Strong transcription	Left Ventricle	heart
27	chr15:99676200-99679800	Strong transcription	A549	lung
28	chr15:99676200-99682600	Weak transcription	NHDF-Ad	bronchial
29	chr15:99676200-99688800	Weak transcription	Brain Angular Gyrus	brain
30	chr15:99676200-99689000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:99676200-99691000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr15:99676200-99696200	Weak transcription	NH-A	brain
33	chr15:99676200-99703400	Weak transcription	GM12878-XiMat	blood
34	chr15:99676400-99680400	Strong transcription	Fetal Stomach	stomach
35	chr15:99676400-99688600	Weak transcription	Fetal Heart	heart
36	chr15:99676400-99690200	Weak transcription	HSMM	muscle
37	chr15:99676600-99679400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:99676600-99679600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:99676600-99679600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:99676600-99679600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:99676600-99679600	Strong transcription	HepG2	liver
42	chr15:99676600-99679800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:99676600-99679800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:99676600-99679800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:99676600-99679800	Strong transcription	Fetal Intestine Small	intestine
46	chr15:99676600-99679800	Strong transcription	Pancreas	Pancrea
47	chr15:99676800-99679000	Strong transcription	Adipose Nuclei	Adipose
48	chr15:99676800-99679200	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:99676800-99679400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:99676800-99679600	Strong transcription	Aorta	Aorta

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