Variant report

Variant	rs3743241
Chromosome Location	chr15:99677357-99677358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:99677192-99677709	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr15:99677060-99678008	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr15:99676989-99677742	Hela-S3	cervix:	n/a	n/a
4	EP300	chr15:99677260-99677832	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr15:99677005-99677916	Hela-S3	cervix:	n/a	n/a
6	MAX	chr15:99677140-99677921	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr15:99677142-99678000	ECC-1	luminal epithelium:	n/a	n/a
8	TCF12	chr15:99677108-99677947	ECC-1	luminal epithelium:	n/a	n/a
9	ZBTB7A	chr15:99677323-99677700	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr15:99676979-99677486	A549	lung:	n/a	n/a
11	POLR2A	chr15:99677058-99677530	PANC-1	pancreas:	n/a	n/a
12	EP300	chr15:99677005-99677991	ECC-1	luminal epithelium:	n/a	n/a
13	JUND	chr15:99677296-99677674	A549	lung:	n/a	n/a
14	TCF12	chr15:99677040-99677936	ECC-1	luminal epithelium:	n/a	n/a
15	USF1	chr15:99677315-99677809	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr15:99677191-99677458	A549	lung:	n/a	n/a
17	NFIC	chr15:99677139-99677936	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:99664100..99665791-chr15:99675684..99677549,2	MCF-7	breast:
2	chr15:99672945..99675578-chr15:99675648..99678258,3	K562	blood:
3	chr15:99676254..99679133-chr15:99680530..99682428,2	K562	blood:
4	chr15:99677279..99681777-chr15:99693510..99696751,5	MCF-7	breast:
5	chr15:99672113..99674481-chr15:99674617..99677492,3	K562	blood:

No data

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

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs181987	1.00[CHB][hapmap]
rs2006920	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs260088	1.00[CHB][hapmap]
rs260089	1.00[CHB][hapmap]
rs260116	1.00[CHB][hapmap]
rs260117	1.00[CHB][hapmap]
rs2623194	0.94[MEX][hapmap]
rs2665082	0.88[MEX][hapmap]
rs34248439	0.84[AMR][1000 genomes]
rs34524139	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4965218	0.89[AMR][1000 genomes]
rs4965444	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4965447	1.00[CHB][hapmap]
rs4965450	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs5030699	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71403425	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71403426	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71403427	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162708	0.88[MEX][hapmap]
rs7167599	1.00[CHB][hapmap]
rs755551	1.00[CHB][hapmap]

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	chr15:99664400-99678800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr15:99664400-99678800	Weak transcription	Brain Germinal Matrix	brain
4	chr15:99664600-99678800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:99664600-99682200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:99664800-99682000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:99664800-99688600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr15:99665000-99683800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:99665000-99714200	Weak transcription	NHEK	skin
10	chr15:99665200-99677400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:99665200-99677400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:99665200-99677600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr15:99665200-99679400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:99665200-99687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:99666000-99683000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:99666200-99680400	Weak transcription	Fetal Brain Female	brain
17	chr15:99666200-99684200	Weak transcription	HSMMtube	muscle
18	chr15:99666400-99679800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
19	chr15:99666800-99677400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:99667600-99679200	Strong transcription	Fetal Muscle Leg	muscle
21	chr15:99669000-99679400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:99670800-99680600	Weak transcription	Thymus	Thymus
23	chr15:99671800-99679200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr15:99673000-99679400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
26	chr15:99673400-99679800	Genic enhancers	Stomach Smooth Muscle	stomach
27	chr15:99674400-99704200	Weak transcription	Fetal Kidney	kidney
28	chr15:99674600-99679800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr15:99676000-99677600	Strong transcription	Colon Smooth Muscle	Colon
30	chr15:99676000-99678200	Strong transcription	Brain Anterior Caudate	brain
31	chr15:99676000-99678600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:99676000-99679000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr15:99676000-99679800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:99676000-99679800	Strong transcription	Fetal Intestine Large	intestine
35	chr15:99676000-99683200	Weak transcription	Stomach Mucosa	stomach
36	chr15:99676200-99677400	Strong transcription	Rectal Smooth Muscle	rectum
37	chr15:99676200-99677600	Weak transcription	Osteobl	bone
38	chr15:99676200-99677800	Strong transcription	Brain Hippocampus Middle	brain
39	chr15:99676200-99679000	Strong transcription	Left Ventricle	heart
40	chr15:99676200-99679800	Strong transcription	A549	lung
41	chr15:99676200-99682600	Weak transcription	NHDF-Ad	bronchial
42	chr15:99676200-99688800	Weak transcription	Brain Angular Gyrus	brain
43	chr15:99676200-99689000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr15:99676200-99691000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr15:99676200-99696200	Weak transcription	NH-A	brain
46	chr15:99676200-99703400	Weak transcription	GM12878-XiMat	blood
47	chr15:99676400-99678400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
48	chr15:99676400-99680400	Strong transcription	Fetal Stomach	stomach
49	chr15:99676400-99688600	Weak transcription	Fetal Heart	heart
50	chr15:99676400-99690200	Weak transcription	HSMM	muscle

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