Variant report

Variant	rs6963499
Chromosome Location	chr7:139442176-139442177
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:139438775..139442827-chr7:139475473..139478721,3	MCF-7	breast:
2	chr7:139441643..139443403-chr7:139444852..139447312,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000059377	Chromatin interaction
ENSG00000064393	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10252208	1.00[MEX][hapmap]
rs10255449	1.00[MEX][hapmap]
rs10261500	1.00[MEX][hapmap]
rs10261757	1.00[MEX][hapmap]
rs10271046	1.00[MEX][hapmap];0.85[MKK][hapmap]
rs10281682	0.85[AMR][1000 genomes]
rs17161128	1.00[MEX][hapmap]
rs17161198	1.00[MEX][hapmap]
rs17161200	1.00[MEX][hapmap]
rs17161201	1.00[MEX][hapmap]
rs17161202	1.00[MEX][hapmap]
rs17161230	1.00[MEX][hapmap]
rs17161272	1.00[MEX][hapmap]
rs1859568	1.00[MEX][hapmap]
rs2158667	1.00[MEX][hapmap]
rs28714444	0.85[AMR][1000 genomes]
rs56086211	0.85[AMR][1000 genomes]
rs6947792	0.90[YRI][hapmap];0.85[AMR][1000 genomes]
rs6954520	0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs6963553	1.00[MEX][hapmap]
rs6964028	1.00[MEX][hapmap]
rs73735619	0.85[AMR][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	nsv1020234	chr7:139377822-139661964	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1032711	chr7:139411404-139684043	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv464732	chr7:139424022-139654256	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv608472	chr7:139424022-139654256	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1018712	chr7:139429703-139658014	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:139432200-139461800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:139432400-139458600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr7:139432800-139469800	Weak transcription	Hela-S3	cervix
4	chr7:139433400-139455800	Enhancers	Brain Angular Gyrus	brain
5	chr7:139434800-139450800	Enhancers	Fetal Heart	heart
6	chr7:139435200-139443600	Enhancers	Fetal Thymus	thymus
7	chr7:139436400-139445400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:139436800-139442200	Enhancers	Duodenum Mucosa	Duodenum
9	chr7:139437600-139452800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:139438000-139444400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:139438000-139444600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr7:139438000-139445200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:139438200-139443400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr7:139438200-139445400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr7:139438200-139451800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:139438400-139444600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:139438400-139445400	Weak transcription	Fetal Lung	lung
18	chr7:139438400-139446600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:139438400-139452600	Weak transcription	Placenta	Placenta
20	chr7:139438400-139462800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr7:139438400-139467000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr7:139438600-139443400	Weak transcription	GM12878-XiMat	blood
23	chr7:139438600-139444800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr7:139438600-139445200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:139438600-139462600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr7:139438800-139466200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr7:139439000-139452600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr7:139439000-139462800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr7:139439400-139442400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr7:139439600-139446600	Enhancers	Stomach Mucosa	stomach
31	chr7:139439800-139450200	Weak transcription	Primary T cells from cord blood	blood
32	chr7:139440200-139442600	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr7:139440400-139443400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr7:139440400-139444600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:139440400-139444800	Enhancers	Liver	Liver
36	chr7:139440400-139446200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr7:139440400-139449200	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr7:139440400-139451400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr7:139440600-139443200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr7:139440600-139444400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr7:139440600-139445200	Weak transcription	Colon Smooth Muscle	Colon
42	chr7:139440600-139454600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr7:139440600-139454600	Weak transcription	Fetal Brain Female	brain
44	chr7:139440600-139456000	Enhancers	Brain Anterior Caudate	brain
45	chr7:139440600-139457600	Enhancers	Brain Substantia Nigra	brain
46	chr7:139440600-139474600	Weak transcription	Fetal Brain Male	brain
47	chr7:139440800-139442600	Weak transcription	Thymus	Thymus
48	chr7:139440800-139442800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr7:139441000-139444400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr7:139441000-139445200	Weak transcription	Brain Germinal Matrix	brain

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