Variant report

Variant	rs17560979
Chromosome Location	chr6:106962853-106962854
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:106956104..106960979-chr6:106961358..106966072,5	MCF-7	breast:
2	chr6:106942291..106945585-chr6:106960604..106964203,3	K562	blood:
3	chr6:106941600..106943967-chr6:106961212..106962868,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112297	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1159148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13193036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13194986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13202942	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13207381	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13218830	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13218960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13219061	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13220097	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[ASN][1000 genomes]
rs17495644	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17495720	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1841688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1841689	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1870866	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2054365	1.00[CHB][hapmap]
rs2297970	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2306099	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2353050	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34590393	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35090908	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35452551	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35546863	0.82[ASN][1000 genomes]
rs35790766	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35843244	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs55858175	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56361614	0.89[ASN][1000 genomes]
rs72941340	0.82[ASN][1000 genomes]
rs7740989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7752730	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[ASN][1000 genomes]
rs7756087	1.00[CHB][hapmap]
rs9320173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9320174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9320175	0.82[ASN][1000 genomes]
rs9480681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9480682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9486381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9486382	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9486383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9486384	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9486385	0.82[ASN][1000 genomes]
rs9486386	0.82[ASN][1000 genomes]
rs9486387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9486388	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1025510	chr6:106791080-106982400	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv538404	chr6:106791080-106982400	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106957400-106963400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr6:106959600-106963400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr6:106959600-106963600	Active TSS	NHEK	skin
4	chr6:106959800-106963200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:106960200-106963200	Active TSS	Duodenum Mucosa	Duodenum
6	chr6:106960200-106963400	Active TSS	Primary T cells fromperipheralblood	blood
7	chr6:106960200-106963400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:106960400-106963200	Active TSS	Placenta	Placenta
9	chr6:106960600-106963400	Flanking Active TSS	Dnd41	blood
10	chr6:106961000-106963400	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr6:106961000-106963600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:106961000-106963600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr6:106961000-106963600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:106961000-106964400	Weak transcription	Spleen	Spleen
15	chr6:106961000-106966800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:106961000-106967800	Weak transcription	Esophagus	oesophagus
17	chr6:106961000-106981000	Weak transcription	Lung	lung
18	chr6:106961000-107001400	Weak transcription	Gastric	stomach
19	chr6:106961200-106963200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr6:106961200-106963800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:106961200-106968600	Weak transcription	Pancreas	Pancrea
22	chr6:106961400-106963400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr6:106961400-106967000	Weak transcription	K562	blood
24	chr6:106961600-106963400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr6:106961600-106963800	Weak transcription	Fetal Thymus	thymus
26	chr6:106961600-106967000	Weak transcription	HSMMtube	muscle
27	chr6:106961800-106963000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr6:106961800-106963600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr6:106962000-106963200	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr6:106962000-106963200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr6:106962000-106963400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:106962000-106966600	Weak transcription	Osteobl	bone
33	chr6:106962000-106972800	Weak transcription	Colon Smooth Muscle	Colon
34	chr6:106962200-106963000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr6:106962200-106963400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:106962200-106963400	Enhancers	Hela-S3	cervix
37	chr6:106962200-106963400	Active TSS	HMEC	breast
38	chr6:106962200-106963800	Enhancers	Fetal Intestine Small	intestine
39	chr6:106962200-106964400	Weak transcription	Small Intestine	intestine
40	chr6:106962200-106966600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:106962200-106966800	Weak transcription	HSMM	muscle
42	chr6:106962200-106967000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr6:106962200-106967000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:106962200-106967000	Weak transcription	Fetal Intestine Large	intestine
45	chr6:106962400-106964800	Enhancers	Stomach Mucosa	stomach
46	chr6:106962400-106966800	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr6:106962400-106967000	Enhancers	Primary T cells from cord blood	blood
48	chr6:106962600-106963000	Enhancers	Adipose Nuclei	Adipose
49	chr6:106962600-106963000	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr6:106962600-106963000	Active TSS	HepG2	liver

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