Variant report

Variant	rs72938245
Chromosome Location	chr2:110316059-110316060
allele	C/T
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	chr2:110310683..110312314-chr2:110314864..110316411,2	MCF-7	breast:
3	chr2:110315967..110317938-chr2:110370785..110372677,2	MCF-7	breast:
4	chr2:110314274..110316891-chr2:110317469..110319541,2	K562	blood:

Variant related genes	Relation type
ENSG00000186522	Chromatin interaction
ENSG00000198142	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs58299134	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61633348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936493	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938300	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940253	1.00[AMR][1000 genomes]
rs72940264	1.00[AMR][1000 genomes]
rs72949182	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949185	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72949187	0.91[AFR][1000 genomes];1.00[AMR][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:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110293200-110316200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:110293400-110331600	Weak transcription	Right Ventricle	heart
3	chr2:110293400-110352200	Weak transcription	Gastric	stomach
4	chr2:110297400-110351600	Weak transcription	Brain Germinal Matrix	brain
5	chr2:110297800-110331800	Weak transcription	Colonic Mucosa	Colon
6	chr2:110299600-110318600	Weak transcription	Esophagus	oesophagus
7	chr2:110299600-110320200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:110299600-110324200	Weak transcription	Brain Angular Gyrus	brain
9	chr2:110301400-110325000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:110301600-110321000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:110302000-110333600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:110302200-110357600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:110302400-110343000	Weak transcription	Psoas Muscle	Psoas
14	chr2:110303000-110320400	Weak transcription	Brain Substantia Nigra	brain
15	chr2:110304200-110318800	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:110304800-110320800	Weak transcription	Fetal Heart	heart
17	chr2:110307200-110322800	Weak transcription	Brain Anterior Caudate	brain
18	chr2:110308200-110317200	Weak transcription	Spleen	Spleen
19	chr2:110308400-110363400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:110308600-110358600	Weak transcription	Small Intestine	intestine
21	chr2:110309000-110347400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr2:110309800-110319800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:110309800-110323000	Weak transcription	Aorta	Aorta
24	chr2:110309800-110351600	Weak transcription	Pancreas	Pancrea
25	chr2:110310200-110318200	Weak transcription	NHLF	lung
26	chr2:110310200-110351600	Weak transcription	Fetal Brain Male	brain
27	chr2:110310400-110317000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr2:110310400-110317800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr2:110310400-110321000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:110310400-110323000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:110310400-110323000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:110310400-110337800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:110310400-110338400	Weak transcription	Lung	lung
34	chr2:110310400-110342000	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:110310400-110351600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:110310400-110351800	Weak transcription	Fetal Brain Female	brain
37	chr2:110310400-110353800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr2:110310400-110363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:110310600-110317000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:110310600-110341400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:110310800-110317000	Weak transcription	HSMMtube	muscle
42	chr2:110310800-110318200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:110310800-110320200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:110310800-110336800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:110312000-110317000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:110312000-110317000	Weak transcription	HSMM	muscle
47	chr2:110312000-110318600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:110312000-110318600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:110312200-110321400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:110312200-110326000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links