Variant report

Variant	rs28599496
Chromosome Location	chr2:110317787-110317788
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:110315553..110317822-chr2:110320975..110322550,2	MCF-7	breast:
2	chr2:110314274..110316891-chr2:110317469..110319541,2	K562	blood:
3	chr2:110316867..110319657-chr2:110370281..110372107,2	MCF-7	breast:
4	chr2:110315967..110317938-chr2:110370785..110372677,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186522	Chromatin interaction
ENSG00000198142	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10195867	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1036317	0.96[ASN][1000 genomes]
rs1036318	0.96[ASN][1000 genomes]
rs10496432	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13006297	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13412327	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1811388	0.96[ASN][1000 genomes]
rs28464093	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28553892	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28570680	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3213866	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34269507	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34311530	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34441132	0.96[ASN][1000 genomes]
rs34517320	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34821058	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35120088	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35223862	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35392016	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35531839	0.83[EUR][1000 genomes]
rs35550721	0.96[ASN][1000 genomes]
rs35834900	1.00[AFR][1000 genomes]
rs35859027	1.00[AFR][1000 genomes]
rs35955221	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4482487	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4953721	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4953729	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4953730	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4953788	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55794045	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56794190	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58031484	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6709945	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6719215	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6725792	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6751785	0.80[ASN][1000 genomes]
rs71425253	1.00[AFR][1000 genomes]
rs72824772	0.88[EUR][1000 genomes]
rs72824788	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72824789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72824796	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72824800	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72824802	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs753492	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7565483	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7577865	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9330317	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9330321	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9750931	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9751648	0.83[EUR][1000 genomes]
rs9752531	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9798179	0.88[EUR][1000 genomes];0.96[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	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv2874	chr2:110289373-110333621	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription 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 miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110293400-110331600	Weak transcription	Right Ventricle	heart
2	chr2:110293400-110352200	Weak transcription	Gastric	stomach
3	chr2:110297400-110351600	Weak transcription	Brain Germinal Matrix	brain
4	chr2:110297800-110331800	Weak transcription	Colonic Mucosa	Colon
5	chr2:110299600-110318600	Weak transcription	Esophagus	oesophagus
6	chr2:110299600-110320200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:110299600-110324200	Weak transcription	Brain Angular Gyrus	brain
8	chr2:110301400-110325000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:110301600-110321000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:110302000-110333600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:110302200-110357600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:110302400-110343000	Weak transcription	Psoas Muscle	Psoas
13	chr2:110303000-110320400	Weak transcription	Brain Substantia Nigra	brain
14	chr2:110304200-110318800	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:110304800-110320800	Weak transcription	Fetal Heart	heart
16	chr2:110307200-110322800	Weak transcription	Brain Anterior Caudate	brain
17	chr2:110308400-110363400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:110308600-110358600	Weak transcription	Small Intestine	intestine
19	chr2:110309000-110347400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr2:110309800-110319800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:110309800-110323000	Weak transcription	Aorta	Aorta
22	chr2:110309800-110351600	Weak transcription	Pancreas	Pancrea
23	chr2:110310200-110318200	Weak transcription	NHLF	lung
24	chr2:110310200-110351600	Weak transcription	Fetal Brain Male	brain
25	chr2:110310400-110317800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:110310400-110321000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:110310400-110323000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:110310400-110323000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:110310400-110337800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:110310400-110338400	Weak transcription	Lung	lung
31	chr2:110310400-110342000	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:110310400-110351600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr2:110310400-110351800	Weak transcription	Fetal Brain Female	brain
34	chr2:110310400-110353800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:110310400-110363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:110310600-110341400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:110310800-110318200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:110310800-110320200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:110310800-110336800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:110312000-110318600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:110312000-110318600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:110312200-110321400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:110312200-110326000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:110312200-110328400	Weak transcription	Ovary	ovary
45	chr2:110312400-110318000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:110313000-110321400	Weak transcription	Fetal Intestine Large	intestine
47	chr2:110313400-110325200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:110313400-110337000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:110313600-110319800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:110313600-110323000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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