Variant report

Variant	rs10902543
Chromosome Location	chr15:99857227-99857228
allele	G/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	CTCF	chr15:99857120-99857270	A549	lung:	n/a	n/a
2	CTCF	chr15:99857105-99857242	MCF-7	breast:	n/a	n/a
3	CTCF	chr15:99857100-99857250	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:99846877..99849995-chr15:99854925..99857345,3	MCF-7	breast:
2	chr15:99856389..99859314-chr15:99863031..99866195,3	MCF-7	breast:
3	chr15:99856565..99859133-chr15:99884132..99886600,2	MCF-7	breast:

Variant related genes	Relation type
LRRC28	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1033035	0.86[JPT][hapmap]
rs1033036	0.91[JPT][hapmap];0.96[YRI][hapmap]
rs10794475	0.82[YRI][hapmap]
rs10902544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11247079	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11247080	0.90[JPT][hapmap]
rs11853278	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11853850	0.85[YRI][hapmap]
rs12592075	0.90[JPT][hapmap];0.96[YRI][hapmap]
rs12906357	0.86[YRI][hapmap]
rs12912927	0.85[JPT][hapmap]
rs12913897	0.90[JPT][hapmap];0.92[YRI][hapmap]
rs1876927	0.91[JPT][hapmap];0.96[YRI][hapmap]
rs2048305	0.81[JPT][hapmap]
rs2089707	0.81[JPT][hapmap]
rs3863401	0.85[JPT][hapmap]
rs4965225	0.81[YRI][hapmap]
rs4965474	0.82[JPT][hapmap]
rs6598237	0.90[JPT][hapmap];0.96[YRI][hapmap]
rs7162949	0.81[YRI][hapmap]
rs7167119	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7167899	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7168227	0.90[JPT][hapmap];0.92[YRI][hapmap]
rs7169906	0.91[JPT][hapmap];0.93[YRI][hapmap]
rs7173844	0.85[JPT][hapmap]
rs7182425	0.84[JPT][hapmap];0.96[YRI][hapmap]
rs7182675	0.91[JPT][hapmap];0.96[YRI][hapmap]
rs8036160	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs8040850	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs8041923	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs8042249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs8042667	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
14	nsv1052528	chr15:99736977-99874210	Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
15	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
16	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
17	nsv1045367	chr15:99781626-99892182	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	25 gene(s)	inside rSNPs	diseases
18	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
19	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

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99793000-99866600	Weak transcription	Gastric	stomach
2	chr15:99833200-99875800	Weak transcription	Thymus	Thymus
3	chr15:99835200-99864200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:99847400-99877200	Weak transcription	Ovary	ovary
5	chr15:99848200-99860800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:99848400-99860600	Weak transcription	HepG2	liver
7	chr15:99848400-99860800	Weak transcription	NH-A	brain
8	chr15:99850400-99863800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:99853000-99876000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr15:99853200-99875400	Weak transcription	Fetal Thymus	thymus
11	chr15:99853600-99875800	Weak transcription	Fetal Intestine Large	intestine
12	chr15:99854200-99860600	Weak transcription	Liver	Liver
13	chr15:99854200-99864200	Weak transcription	Left Ventricle	heart
14	chr15:99854400-99860600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr15:99854400-99863600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:99854400-99864000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr15:99854400-99876000	Weak transcription	Dnd41	blood
18	chr15:99856200-99857800	Weak transcription	HUVEC	blood vessel
19	chr15:99856200-99860400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:99856200-99860400	Weak transcription	HMEC	breast
21	chr15:99856200-99860400	Weak transcription	NHEK	skin
22	chr15:99856200-99860600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:99856200-99860600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:99856800-99860800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:99857200-99859600	Weak transcription	A549	lung

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