Variant report

Variant	rs13085247
Chromosome Location	chr3:142242257-142242258
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142241940..142244885-chr3:142296326..142298965,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10935463	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1129391	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11708470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715514	0.90[EUR][1000 genomes]
rs11718899	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11916455	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11923612	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12629001	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12629713	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12634255	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12638158	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12639363	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13063075	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13065800	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13066441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068397	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13070239	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13072346	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13072355	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13075259	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13085261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089219	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13092234	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13092593	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13093304	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13099184	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2227929	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2227931	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923464	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4256152	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4558780	0.91[EUR][1000 genomes]
rs4582075	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6440085	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776402	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7432464	0.84[ASN][1000 genomes]
rs7630115	0.84[EUR][1000 genomes]
rs7636909	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7641914	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers 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	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv933680	chr3:142211643-142287189	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142200400-142243800	Weak transcription	Fetal Heart	heart
2	chr3:142200600-142271800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:142201600-142273200	Weak transcription	Esophagus	oesophagus
4	chr3:142201800-142243600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:142201800-142273800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:142203000-142255200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:142203800-142255200	Weak transcription	Gastric	stomach
8	chr3:142204200-142253000	Weak transcription	Brain Substantia Nigra	brain
9	chr3:142204200-142273200	Weak transcription	Spleen	Spleen
10	chr3:142204200-142281400	Weak transcription	Colonic Mucosa	Colon
11	chr3:142209400-142271800	Weak transcription	HepG2	liver
12	chr3:142212000-142251400	Weak transcription	Brain Anterior Caudate	brain
13	chr3:142218200-142251200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:142220200-142251200	Weak transcription	NHDF-Ad	bronchial
15	chr3:142220200-142252400	Weak transcription	NHLF	lung
16	chr3:142220600-142253000	Weak transcription	HMEC	breast
17	chr3:142220800-142251400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:142221000-142249400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:142226000-142287200	Weak transcription	Right Ventricle	heart
20	chr3:142226400-142251800	Weak transcription	Lung	lung
21	chr3:142226600-142251000	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:142226600-142252200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:142228600-142252600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:142228600-142253000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:142229000-142244400	Weak transcription	Pancreas	Pancrea
26	chr3:142230600-142243000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:142231600-142255200	Weak transcription	Aorta	Aorta
28	chr3:142231600-142295800	Weak transcription	Small Intestine	intestine
29	chr3:142233000-142252000	Weak transcription	HUVEC	blood vessel
30	chr3:142233200-142251000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:142233200-142251600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:142233600-142255200	Weak transcription	Fetal Stomach	stomach
33	chr3:142233600-142271000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:142235200-142251000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:142236000-142244200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:142237200-142243600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr3:142237800-142251800	Weak transcription	Hela-S3	cervix
38	chr3:142238000-142243200	Strong transcription	Adipose Nuclei	Adipose
39	chr3:142238400-142242400	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:142238400-142242400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:142238600-142243000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:142238600-142269000	Weak transcription	Fetal Intestine Small	intestine
43	chr3:142238800-142242400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:142239000-142243000	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr3:142239800-142269600	Weak transcription	Thymus	Thymus
46	chr3:142240400-142242400	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:142240600-142242400	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:142240600-142242400	Strong transcription	Dnd41	blood
49	chr3:142240600-142251400	Weak transcription	Brain Angular Gyrus	brain
50	chr3:142240800-142242400	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links