Variant report

Variant	rs2290446
Chromosome Location	chr15:100246618-100246619
allele	C/T
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	STAT3	chr15:100246525-100246725	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr15:100246102-100247960	GM12878	blood:	n/a	n/a
3	RUNX3	chr15:100246606-100247130	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:100105316..100107211-chr15:100246606..100248832,2	MCF-7	breast:
2	chr15:99790531..99793156-chr15:100244093..100247016,2	MCF-7	breast:
3	chr15:100104091..100109623-chr15:100241901..100248412,10	MCF-7	breast:

Variant related genes	Relation type
MEF2A	TF binding region
ENSG00000168904	Chromatin interaction
ENSG00000068305	Chromatin interaction
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12900424	0.93[ASN][1000 genomes]
rs12913446	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12915690	0.89[ASN][1000 genomes]
rs12916795	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs34222295	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs34513363	0.84[ASN][1000 genomes]
rs34987456	0.94[ASN][1000 genomes]
rs35043171	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35295124	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs35357315	0.93[ASN][1000 genomes]
rs35480704	0.93[ASN][1000 genomes]
rs35487956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35585008	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs35655388	0.93[ASN][1000 genomes]
rs35912172	0.85[ASN][1000 genomes]
rs3730280	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3784450	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs67074319	0.83[ASN][1000 genomes]
rs67381509	0.93[ASN][1000 genomes]
rs67593144	0.93[ASN][1000 genomes]
rs71403454	0.87[ASN][1000 genomes]
rs71403455	0.94[ASN][1000 genomes]
rs8024380	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs8030451	0.88[ASN][1000 genomes]
rs8036677	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	47 gene(s)	inside rSNPs	diseases
3	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1038005	chr15:100170414-100633714	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv542522	chr15:100170414-100633714	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv904559	chr15:100174907-100255046	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv904560	chr15:100196657-100339331	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
8	nsv904561	chr15:100204918-100486828	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv428313	chr15:100236203-100757039	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv904563	chr15:100239546-100274747	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
11	nsv570730	chr15:100240910-100700520	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription 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	22 gene(s)	inside rSNPs	diseases
12	nsv1045838	chr15:100243067-101032218	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	nsv904564	chr15:100245296-100723798	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100159000-100253000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:100171200-100248800	Weak transcription	Gastric	stomach
3	chr15:100213200-100250800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:100219400-100248200	Weak transcription	Small Intestine	intestine
5	chr15:100219600-100248400	Weak transcription	Spleen	Spleen
6	chr15:100223600-100247400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:100223800-100246800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr15:100231000-100250600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:100233200-100246800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr15:100233400-100247000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr15:100233400-100247000	Weak transcription	Fetal Stomach	stomach
12	chr15:100233400-100247000	Weak transcription	Left Ventricle	heart
13	chr15:100233400-100247200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:100233400-100247400	Weak transcription	Psoas Muscle	Psoas
15	chr15:100233400-100247600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:100233400-100248400	Weak transcription	Right Ventricle	heart
17	chr15:100233400-100248800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:100233400-100248800	Weak transcription	Esophagus	oesophagus
19	chr15:100233400-100248800	Weak transcription	Fetal Intestine Small	intestine
20	chr15:100233400-100248800	Weak transcription	Lung	lung
21	chr15:100233400-100248800	Weak transcription	Ovary	ovary
22	chr15:100233400-100248800	Weak transcription	Pancreas	Pancrea
23	chr15:100233400-100250600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:100233400-100250800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr15:100233400-100251200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:100233600-100248800	Weak transcription	Fetal Brain Male	brain
27	chr15:100233800-100250800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr15:100233800-100256600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:100234200-100247000	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:100234800-100248400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr15:100235000-100248800	Weak transcription	Colonic Mucosa	Colon
32	chr15:100235200-100250800	Weak transcription	Brain Germinal Matrix	brain
33	chr15:100236600-100247400	Weak transcription	Fetal Brain Female	brain
34	chr15:100236600-100250800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:100236800-100249200	Weak transcription	Placenta	Placenta
36	chr15:100237000-100247000	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr15:100237000-100250000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:100237200-100250200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr15:100241000-100247400	Weak transcription	Right Atrium	heart
40	chr15:100241800-100248800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr15:100243600-100246800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr15:100244200-100247400	Enhancers	Fetal Thymus	thymus
43	chr15:100244400-100250200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:100244400-100250800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:100244600-100247000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:100244600-100247000	Weak transcription	NHEK	skin
47	chr15:100244600-100247200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:100244600-100247200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:100244600-100247200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:100244600-100247200	Weak transcription	HSMMtube	muscle

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