Variant report

Variant	rs2242415
Chromosome Location	chr5:17225333-17225334
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:17221834..17224363-chr5:17224517..17226691,2	MCF-7	breast:
2	chr5:17223288..17225551-chr5:17303206..17305533,2	MCF-7	breast:
3	chr5:17224192..17226114-chr5:17256791..17258663,2	MCF-7	breast:
4	chr5:17224329..17226493-chr5:18018775..18020454,2	MCF-7	breast:
5	chr5:17223694..17225460-chr5:17227873..17230448,2	K562	blood:
6	chr5:17223199..17226233-chr5:17226952..17230155,3	MCF-7	breast:
7	chr5:17223492..17225946-chr5:17474747..17476783,2	MCF-7	breast:
8	chr5:17214960..17221110-chr5:17221778..17226388,13	MCF-7	breast:
9	chr5:17223132..17225372-chr5:17261877..17263597,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000176788	Chromatin interaction
ENSG00000215196	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1105298	0.87[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2291236	0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4288115	0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs62348040	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7733967	0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv830218	chr5:17093162-17290045	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1029959	chr5:17133214-17455995	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv521697	chr5:17211649-17225333	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv597312	chr5:17214901-17225333	Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17218800-17225400	Transcr. at gene 5' and 3'	A549	lung
2	chr5:17219800-17231800	Weak transcription	Fetal Kidney	kidney
3	chr5:17219800-17233600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr5:17220200-17225400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:17220200-17225400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr5:17220400-17225400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr5:17220400-17229400	Weak transcription	Brain Anterior Caudate	brain
8	chr5:17221000-17227000	Genic enhancers	Hela-S3	cervix
9	chr5:17221400-17228200	Weak transcription	HUVEC	blood vessel
10	chr5:17222000-17227000	Flanking Active TSS	GM12878-XiMat	blood
11	chr5:17222200-17225600	Enhancers	H1 Cell Line	embryonic stem cell
12	chr5:17222600-17225800	Enhancers	NHLF	lung
13	chr5:17222600-17228800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr5:17222600-17228800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr5:17222800-17227800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:17222800-17239000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:17223200-17225400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:17223200-17225800	Enhancers	Placenta	Placenta
19	chr5:17223200-17235800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr5:17223400-17226800	Enhancers	Fetal Brain Male	brain
21	chr5:17223400-17229400	Weak transcription	Fetal Thymus	thymus
22	chr5:17223600-17225800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:17223600-17225800	Flanking Active TSS	Fetal Brain Female	brain
24	chr5:17223600-17230400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:17223800-17225600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr5:17223800-17225600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:17224000-17225400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:17224000-17225800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:17224000-17226000	Enhancers	Primary B cells from cord blood	blood
30	chr5:17224000-17226200	Enhancers	Primary B cells from peripheral blood	blood
31	chr5:17224000-17226800	Genic enhancers	NHEK	skin
32	chr5:17224000-17227800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr5:17224200-17228600	Weak transcription	Ovary	ovary
34	chr5:17224400-17225400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr5:17224400-17225800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:17224400-17225800	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr5:17224400-17225800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:17224400-17227000	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr5:17224400-17227800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:17224400-17227800	Weak transcription	HMEC	breast
41	chr5:17224400-17233400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:17224600-17225400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:17224600-17226000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr5:17224600-17226000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr5:17224600-17226200	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr5:17224800-17225400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:17224800-17225400	Flanking Active TSS	HSMM	muscle
48	chr5:17224800-17225600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr5:17224800-17225600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:17224800-17225600	Flanking Active TSS	Osteobl	bone

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