Variant report

Variant	rs7225249
Chromosome Location	chr17:20104191-20104192
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:20058170..20060902-chr17:20103752..20106651,2	MCF-7	breast:
2	chr17:20080334..20082016-chr17:20102428..20104693,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128487	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11204422	0.89[JPT][hapmap]
rs11654025	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs11870381	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs11870673	0.84[ASN][1000 genomes]
rs12451216	0.85[ASN][1000 genomes]
rs12451841	0.90[JPT][hapmap]
rs12947713	0.91[JPT][hapmap]
rs17686798	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs17759959	0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2034110	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs35041742	0.85[ASN][1000 genomes]
rs36051592	0.87[ASN][1000 genomes]
rs3940274	0.84[ASN][1000 genomes]
rs4924808	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs4925075	0.90[JPT][hapmap]
rs4925082	0.90[JPT][hapmap]
rs4925088	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs57146223	0.96[ASN][1000 genomes]
rs6587207	0.91[JPT][hapmap]
rs7207459	0.91[JPT][hapmap]
rs7215803	0.90[JPT][hapmap]
rs7223363	0.85[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7224875	0.90[JPT][hapmap]
rs8066705	0.88[ASN][1000 genomes]
rs8068484	0.91[JPT][hapmap]
rs8074791	0.88[ASN][1000 genomes]
rs8075343	0.91[JPT][hapmap]
rs8080190	0.90[JPT][hapmap]
rs8080573	1.00[AMR][1000 genomes]
rs888424	0.90[JPT][hapmap]
rs972966	0.88[ASN][1000 genomes]
rs9915039	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
3	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv482830	chr17:20012748-20169153	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer 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	10 gene(s)	inside rSNPs	diseases
9	nsv833396	chr17:20029183-20150808	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking 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	8 gene(s)	inside rSNPs	diseases
10	nsv428669	chr17:20071969-20245033	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1057870	chr17:20079146-20121848	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1064854	chr17:20086562-20225751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	esv2761953	chr17:20086562-20225763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1063833	chr17:20088333-20206601	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv574581	chr17:20088492-20699545	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20094200-20105400	Weak transcription	Gastric	stomach
2	chr17:20094600-20105400	Weak transcription	K562	blood
3	chr17:20094800-20105600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:20095400-20104800	Weak transcription	HMEC	breast
5	chr17:20097600-20107800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr17:20099800-20107200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr17:20101600-20107600	Enhancers	Hela-S3	cervix
8	chr17:20101600-20108200	Weak transcription	Aorta	Aorta
9	chr17:20101800-20107000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr17:20102000-20118400	Weak transcription	Pancreas	Pancrea
11	chr17:20102200-20104400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr17:20102200-20105000	Weak transcription	GM12878-XiMat	blood
13	chr17:20102400-20106400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr17:20102400-20107000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr17:20102400-20107200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:20102400-20108200	Weak transcription	Adipose Nuclei	Adipose
17	chr17:20102400-20115200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr17:20102600-20108200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr17:20103000-20104400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr17:20103000-20109200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr17:20103200-20107600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr17:20103200-20107800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr17:20103400-20104800	Enhancers	Brain Angular Gyrus	brain
24	chr17:20103400-20105000	Enhancers	A549	lung
25	chr17:20103400-20105200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr17:20103400-20105600	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr17:20103400-20107600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr17:20103400-20107600	Enhancers	Brain Hippocampus Middle	brain
29	chr17:20103400-20107800	Enhancers	Osteobl	bone
30	chr17:20103600-20104200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr17:20103600-20104200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr17:20103600-20104200	Enhancers	HSMM	muscle
33	chr17:20103600-20104600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr17:20103600-20104800	Enhancers	Fetal Brain Male	brain
35	chr17:20103600-20105200	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr17:20103600-20105400	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr17:20103600-20107400	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr17:20103600-20107600	Enhancers	Brain Cingulate Gyrus	brain
39	chr17:20103600-20107600	Enhancers	Brain Substantia Nigra	brain
40	chr17:20103600-20107800	Enhancers	Brain Anterior Caudate	brain
41	chr17:20103600-20111600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr17:20103800-20104200	Enhancers	H9 Cell Line	embryonic stem cell
43	chr17:20103800-20104200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr17:20103800-20104200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr17:20103800-20104200	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr17:20103800-20104600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr17:20103800-20104600	Enhancers	Fetal Brain Female	brain
48	chr17:20103800-20104800	Enhancers	Ovary	ovary
49	chr17:20103800-20105000	Weak transcription	NH-A	brain
50	chr17:20103800-20105400	Enhancers	Rectal Mucosa Donor 29	rectum

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