Variant report

Variant	rs13327125
Chromosome Location	chr3:120066393-120066394
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119962878..119965844-chr3:120065668..120069448,4	MCF-7	breast:
2	chr3:120055756..120058586-chr3:120065980..120068170,2	K562	blood:
3	chr3:120066130..120068617-chr3:120117930..120119437,2	K562	blood:
4	chr3:120002820..120005702-chr3:120066388..120068289,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163430	Chromatin interaction
ENSG00000175697	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10048964	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1085614	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1085616	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1085617	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1147681	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1147688	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1147689	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1147690	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1147697	0.81[AMR][1000 genomes]
rs11914405	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11928731	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13318758	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13318838	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1625178	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1716855	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1716856	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1733326	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1733328	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2638597	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28535957	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28826066	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6764516	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6767308	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6777979	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6799005	0.86[AMR][1000 genomes]
rs6808913	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs787186	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs787187	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs787190	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs787192	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs787193	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs787196	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs787205	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs787206	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs787207	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs787208	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs809792	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs923729	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs951658	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9810151	0.81[AMR][1000 genomes]
rs9810784	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9822636	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9822759	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9851711	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9856670	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9860676	0.81[AMR][1000 genomes]
rs9876547	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer 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 miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv236293	chr3:120066250-120069861	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120026800-120067200	Weak transcription	Aorta	Aorta
2	chr3:120033200-120067000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:120044400-120066800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:120045200-120066800	Weak transcription	Stomach Mucosa	stomach
5	chr3:120045600-120066800	Weak transcription	Colonic Mucosa	Colon
6	chr3:120048400-120066800	Weak transcription	Right Ventricle	heart
7	chr3:120051000-120067000	Weak transcription	Esophagus	oesophagus
8	chr3:120051200-120066800	Weak transcription	Psoas Muscle	Psoas
9	chr3:120051200-120066800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:120052600-120067000	Weak transcription	Left Ventricle	heart
11	chr3:120053200-120066600	Weak transcription	Fetal Kidney	kidney
12	chr3:120053800-120066600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:120053800-120066600	Weak transcription	NH-A	brain
14	chr3:120054200-120066600	Weak transcription	HUVEC	blood vessel
15	chr3:120054200-120066600	Weak transcription	K562	blood
16	chr3:120057800-120067000	Weak transcription	Small Intestine	intestine
17	chr3:120058600-120066600	Weak transcription	Fetal Lung	lung
18	chr3:120059000-120066800	Weak transcription	Placenta	Placenta
19	chr3:120060800-120066600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:120061000-120066600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:120061200-120066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:120061200-120066600	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:120061400-120066800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:120061400-120066800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:120061400-120066800	Weak transcription	Gastric	stomach
26	chr3:120061400-120067000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:120061600-120066400	Weak transcription	Pancreas	Pancrea
28	chr3:120061600-120066600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:120061600-120066600	Weak transcription	Fetal Intestine Small	intestine
30	chr3:120061600-120066800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:120061600-120067000	Weak transcription	Spleen	Spleen
32	chr3:120061800-120066600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:120061800-120066800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr3:120062000-120066600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:120062000-120066600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:120062000-120066600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:120062000-120066600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:120062000-120066600	Weak transcription	Thymus	Thymus
39	chr3:120062000-120066800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:120062000-120066800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:120062400-120066800	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr3:120062600-120066800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr3:120062600-120066800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:120062600-120066800	Weak transcription	HSMM	muscle
45	chr3:120062800-120066600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:120062800-120066600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr3:120062800-120066600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr3:120063000-120067000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr3:120063200-120066600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:120063200-120066600	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links