Variant report

Variant	rs17839548
Chromosome Location	chr16:30564526-30564527
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30553506..30556409-chr16:30563920..30565827,2	MCF-7	breast:
2	chr16:30534557..30548684-chr16:30561877..30572653,49	MCF-7	breast:
3	chr16:30563954..30565557-chr16:30582718..30585248,2	MCF-7	breast:
4	chr16:30564268..30564883-chr6:153979585..153980484,2	MCF-7	breast:
5	chr16:30409685..30411785-chr16:30564140..30566848,3	MCF-7	breast:
6	chr16:30564382..30566919-chr16:30582116..30584328,2	MCF-7	breast:
7	chr16:30549147..30550840-chr16:30563240..30565616,2	MCF-7	breast:
8	chr16:30560063..30566215-chr16:30567475..30571582,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000229809	Chromatin interaction
ENSG00000235560	Chromatin interaction
ENSG00000239791	Chromatin interaction
ENSG00000169957	Chromatin interaction
ENSG00000169955	Chromatin interaction
ENSG00000169951	Chromatin interaction
ENSG00000260869	Chromatin interaction
ENSG00000261459	Chromatin interaction
ENSG00000260494	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs4243233	1.00[CHD][hapmap]
rs56153335	1.00[ASN][1000 genomes]
rs59151595	1.00[ASN][1000 genomes]
rs6565191	1.00[ASN][1000 genomes]
rs6565193	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72793351	1.00[ASN][1000 genomes]
rs8056929	0.87[GIH][hapmap]
rs8060136	1.00[MEX][hapmap]
rs8063005	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9673428	1.00[ASN][1000 genomes]
rs9924077	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9934806	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9937653	1.00[MEX][hapmap]

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	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
2	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
4	esv3390311	chr16:30544451-30567432	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	n/a
5	esv3432040	chr16:30545881-30569546	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
6	nsv905727	chr16:30564526-30689696	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30548000-30564600	Weak transcription	Primary B cells from cord blood	blood
2	chr16:30553200-30565200	Weak transcription	Fetal Lung	lung
3	chr16:30553400-30568400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr16:30553600-30564800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr16:30553600-30565600	Weak transcription	Pancreas	Pancrea
6	chr16:30553600-30567400	Weak transcription	Hela-S3	cervix
7	chr16:30554000-30565200	Weak transcription	Colon Smooth Muscle	Colon
8	chr16:30555000-30568600	Weak transcription	Fetal Kidney	kidney
9	chr16:30556600-30565600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr16:30556800-30568600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr16:30560400-30564600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr16:30560400-30565200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr16:30560400-30565400	Weak transcription	Stomach Mucosa	stomach
14	chr16:30560400-30565800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr16:30560400-30568600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr16:30560600-30565800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr16:30560600-30565800	Weak transcription	NHLF	lung
18	chr16:30560800-30564800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr16:30560800-30564800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr16:30560800-30564800	Weak transcription	Osteobl	bone
21	chr16:30560800-30565200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr16:30560800-30565800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr16:30560800-30568400	Weak transcription	NHEK	skin
24	chr16:30561000-30564800	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr16:30561000-30565000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr16:30561000-30568600	Weak transcription	HSMM	muscle
27	chr16:30561000-30568600	Weak transcription	NH-A	brain
28	chr16:30561600-30567000	Weak transcription	Fetal Heart	heart
29	chr16:30562200-30566200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr16:30562200-30566400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr16:30562400-30564600	Enhancers	Primary T cells from cord blood	blood
32	chr16:30562400-30564600	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr16:30562400-30564600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr16:30562400-30564800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr16:30562400-30565600	Weak transcription	Brain Angular Gyrus	brain
36	chr16:30562600-30564600	Enhancers	Right Ventricle	heart
37	chr16:30562600-30567400	Genic enhancers	Fetal Intestine Small	intestine
38	chr16:30562600-30567600	Strong transcription	Fetal Stomach	stomach
39	chr16:30562800-30564800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr16:30563000-30564800	Weak transcription	Aorta	Aorta
41	chr16:30563000-30565200	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr16:30563200-30564800	Enhancers	HepG2	liver
43	chr16:30563200-30567600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr16:30563400-30564800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr16:30563400-30565000	Weak transcription	GM12878-XiMat	blood
46	chr16:30563400-30567600	Weak transcription	Fetal Brain Male	brain
47	chr16:30563400-30568600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr16:30563600-30564600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr16:30563600-30564800	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr16:30563600-30565000	Enhancers	Primary T cells fromperipheralblood	blood

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