Variant report

Variant	rs72940099
Chromosome Location	chr3:112292674-112292675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112285735..112289374-chr3:112291760..112294225,3	K562	blood:
2	chr3:112285735..112288489-chr3:112291503..112294225,2	K562	blood:
3	chr3:112281244..112282995-chr3:112290178..112292787,2	K562	blood:
4	chr3:112290282..112294480-chr3:112295112..112298665,4	K562	blood:
5	chr3:112289268..112293035-chr3:112358216..112361029,3	MCF-7	breast:
6	chr3:112290552..112292970-chr3:112296828..112298665,2	K562	blood:
7	chr3:112291247..112293623-chr3:112708463..112710312,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091986	Chromatin interaction
ENSG00000272844	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000138459	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs13070342	0.94[AFR][1000 genomes]
rs57937078	1.00[AMR][1000 genomes]
rs59090018	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938420	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938422	1.00[AMR][1000 genomes]
rs72938432	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938438	1.00[AMR][1000 genomes]
rs72938454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72938498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72940091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942068	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942074	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942077	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942080	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942089	1.00[AMR][1000 genomes]
rs72943904	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112281800-112299400	Weak transcription	Left Ventricle	heart
2	chr3:112281800-112301600	Weak transcription	HepG2	liver
3	chr3:112281800-112312000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:112281800-112315400	Weak transcription	Pancreas	Pancrea
5	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
6	chr3:112281800-112325400	Weak transcription	Gastric	stomach
7	chr3:112282000-112312200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
10	chr3:112282200-112303400	Weak transcription	Psoas Muscle	Psoas
11	chr3:112282400-112299400	Weak transcription	Fetal Stomach	stomach
12	chr3:112282400-112301600	Weak transcription	Hela-S3	cervix
13	chr3:112282400-112304400	Weak transcription	Fetal Heart	heart
14	chr3:112282400-112306600	Weak transcription	Right Ventricle	heart
15	chr3:112282400-112307200	Weak transcription	Small Intestine	intestine
16	chr3:112282400-112312400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:112282400-112316800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:112282400-112322800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:112282400-112324200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:112282600-112297200	Weak transcription	Thymus	Thymus
22	chr3:112282600-112298200	Weak transcription	NHEK	skin
23	chr3:112282600-112301200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:112282600-112301400	Weak transcription	A549	lung
25	chr3:112282600-112306800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:112282800-112298600	Weak transcription	Brain Angular Gyrus	brain
27	chr3:112282800-112301400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:112282800-112302200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:112283000-112299200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:112283000-112301800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:112283000-112316400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr3:112283600-112295800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:112283800-112295400	Strong transcription	Liver	Liver
34	chr3:112284000-112297600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr3:112284000-112298600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:112284200-112293600	Strong transcription	Fetal Thymus	thymus
37	chr3:112284400-112294400	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:112284600-112294600	Weak transcription	Fetal Intestine Small	intestine
39	chr3:112284800-112294200	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:112285200-112293400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:112285200-112294400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr3:112285200-112294600	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:112286200-112294200	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr3:112286400-112293000	Strong transcription	Fetal Intestine Large	intestine
45	chr3:112286400-112293600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr3:112286400-112294000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:112286400-112294000	Strong transcription	Fetal Brain Female	brain
48	chr3:112286600-112293400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:112286600-112298000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:112287000-112293200	Strong transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links