Variant report

Variant	rs2085446
Chromosome Location	chr3:138293291-138293292
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	chr3:138291466..138294081-chr3:138311931..138314482,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114107	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10935287	0.80[ASN][1000 genomes]
rs11717771	0.81[ASN][1000 genomes]
rs11916525	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054428	0.82[EUR][1000 genomes]
rs12630060	0.91[EUR][1000 genomes]
rs12630144	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12630351	0.87[EUR][1000 genomes]
rs12632793	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12632794	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12635354	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12635490	0.91[EUR][1000 genomes]
rs12635904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636936	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12637638	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12637679	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs13059817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062423	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13067095	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13067864	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13069355	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13072751	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13073978	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13077766	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13084780	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13093668	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13095122	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13095125	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098554	0.87[EUR][1000 genomes]
rs1563615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1672928	0.82[ASN][1000 genomes]
rs1672931	0.84[ASN][1000 genomes]
rs1672936	0.82[ASN][1000 genomes]
rs1673608	0.80[ASN][1000 genomes]
rs2085447	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280596	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34011134	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34153951	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34284415	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34316974	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34377792	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34416776	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34482601	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34583117	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34607531	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34640717	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34652182	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34878008	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35034861	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35269190	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35270255	0.87[EUR][1000 genomes]
rs35340237	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35489558	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35537868	0.91[EUR][1000 genomes]
rs35549884	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35597846	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35834585	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35876758	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35906980	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3773748	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56028542	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56654955	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57516770	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58873565	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59184769	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59371015	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60371967	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60426689	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61258082	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61662147	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs654528	0.84[ASN][1000 genomes]
rs66775405	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67390774	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67666216	0.90[ASN][1000 genomes]
rs6784770	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73229540	0.86[ASN][1000 genomes]
rs773450	0.81[ASN][1000 genomes]
rs773455	0.86[ASN][1000 genomes]
rs9049	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs936316	0.80[ASN][1000 genomes]
rs9880928	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv522517	chr3:138174523-138297982	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv877538	chr3:138218709-138311201	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
11	esv3429877	chr3:138272946-138325019	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
12	esv3448925	chr3:138277303-138312046	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138268600-138297800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:138269000-138306800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:138278800-138296200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr3:138279000-138296800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:138279000-138298400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:138279600-138297800	Weak transcription	Right Ventricle	heart
7	chr3:138279600-138300400	Weak transcription	Colonic Mucosa	Colon
8	chr3:138279800-138296400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:138280000-138296400	Weak transcription	Primary T cells from cord blood	blood
10	chr3:138280000-138297000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:138280000-138297800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:138280000-138311200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:138280200-138296400	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:138282000-138296400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr3:138285200-138307200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:138286000-138297200	Weak transcription	Osteobl	bone
17	chr3:138286600-138296800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr3:138286800-138297800	Weak transcription	HepG2	liver
19	chr3:138288200-138299400	Weak transcription	HSMM	muscle
20	chr3:138288200-138312400	Weak transcription	Ovary	ovary
21	chr3:138289000-138310600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:138289400-138298000	Weak transcription	Brain Anterior Caudate	brain
23	chr3:138289600-138298200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr3:138290200-138312400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:138291000-138293400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:138291000-138294200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:138291200-138296600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr3:138291200-138296800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:138291200-138310000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:138291400-138293400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
31	chr3:138291400-138293600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
32	chr3:138291400-138294000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:138291600-138293400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
34	chr3:138291600-138293400	ZNF genes & repeats	Brain Germinal Matrix	brain
35	chr3:138291800-138293800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
36	chr3:138292000-138293400	ZNF genes & repeats	Adipose Nuclei	Adipose
37	chr3:138292200-138304400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:138292800-138293400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:138292800-138293400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:138292800-138293600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:138292800-138293600	ZNF genes & repeats	Thymus	Thymus
42	chr3:138292800-138293800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
43	chr3:138292800-138293800	ZNF genes & repeats	Fetal Intestine Small	intestine
44	chr3:138292800-138293800	ZNF genes & repeats	Fetal Stomach	stomach
45	chr3:138292800-138294000	ZNF genes & repeats	Fetal Thymus	thymus
46	chr3:138293000-138293400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:138293000-138293400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:138293000-138293400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
49	chr3:138293000-138296600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:138293000-138296800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links