Variant report

Variant	rs1129391
Chromosome Location	chr3:142283766-142283767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:142283758-142283766	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142282794..142284400-chr3:142286449..142288968,2	K562	blood:

Variant related genes	Relation type
ATR	TF binding region

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

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

rs_ID	r²[population]
rs10935463	0.81[EUR][1000 genomes]
rs11708470	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11715514	0.82[EUR][1000 genomes]
rs11718899	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11916455	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11923612	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12629001	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12629713	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12634255	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12638158	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12639363	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13063075	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13065800	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13066441	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13068397	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13070239	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13072346	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13072355	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13075259	0.81[EUR][1000 genomes]
rs13085247	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13085261	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13089219	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13092234	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13092593	0.86[EUR][1000 genomes]
rs13093304	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13099184	0.81[EUR][1000 genomes]
rs2227929	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2227931	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3923464	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4256152	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4558780	0.83[EUR][1000 genomes]
rs4582075	0.84[EUR][1000 genomes]
rs6440085	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6776402	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7432464	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7630115	0.81[ASN][1000 genomes]
rs7636909	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7641914	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142226000-142287200	Weak transcription	Right Ventricle	heart
2	chr3:142231600-142295800	Weak transcription	Small Intestine	intestine
3	chr3:142244400-142295600	Weak transcription	Fetal Heart	heart
4	chr3:142248400-142287400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:142253400-142284800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:142253400-142284800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:142253800-142296400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:142259800-142285600	Strong transcription	Dnd41	blood
9	chr3:142263000-142285400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr3:142263400-142286200	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr3:142263600-142288000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:142263800-142285600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:142263800-142286600	Strong transcription	Liver	Liver
14	chr3:142264000-142285200	Strong transcription	Fetal Thymus	thymus
15	chr3:142265200-142285000	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:142265200-142287600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:142266400-142285600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr3:142267000-142286600	Strong transcription	Primary B cells from cord blood	blood
19	chr3:142267800-142285200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:142268800-142284200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:142269200-142292600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr3:142270000-142287200	Weak transcription	Pancreas	Pancrea
23	chr3:142270200-142285000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:142270800-142285200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:142270800-142286400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:142271000-142285400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:142271800-142285200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:142272200-142286200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:142272600-142284800	Weak transcription	HepG2	liver
30	chr3:142272600-142287400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:142272600-142296200	Weak transcription	Brain Angular Gyrus	brain
32	chr3:142272600-142296200	Weak transcription	Psoas Muscle	Psoas
33	chr3:142272800-142293400	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr3:142274000-142284800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:142274000-142285200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:142274000-142286600	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr3:142274000-142287200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:142274000-142287400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:142274000-142287400	Weak transcription	Gastric	stomach
40	chr3:142274000-142287400	Weak transcription	Lung	lung
41	chr3:142274200-142285000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:142274200-142285200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:142274200-142287600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr3:142274400-142285000	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:142274800-142296200	Weak transcription	NHLF	lung
46	chr3:142274800-142296400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:142275000-142293600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:142275400-142285000	Weak transcription	Brain Anterior Caudate	brain
49	chr3:142275400-142285000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:142275600-142296400	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links