Variant report

Variant	rs1583654
Chromosome Location	chr3:120317469-120317470
allele	A/G
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	chr3:120317106-120323167	K562	blood:	n/a	n/a
2	POLR2A	chr3:120317343-120317927	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr3:120317440-120317646	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:120317420-120317709	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120315040..120318401-chr3:120459431..120463263,5	MCF-7	breast:
2	chr3:120313507..120317684-chr3:120458763..120463692,6	MCF-7	breast:

Variant related genes	Relation type
NDUFB4	TF binding region
ENSG00000153767	Chromatin interaction
ENSG00000144840	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12635956	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1465837	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16831523	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17140281	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17140284	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34438738	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34924588	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35085316	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72625410	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72625411	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72625413	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72625414	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72625415	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72625416	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626272	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][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	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
2	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
3	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
4	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv508238	chr3:120248574-120329424	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	esv3373301	chr3:120273762-120421260	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	nsv877377	chr3:120287683-120426750	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	esv3464294	chr3:120303062-120420810	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	esv3464295	chr3:120303062-120420810	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120315800-120320200	Weak transcription	Pancreas	Pancrea
2	chr3:120315800-120323600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:120315800-120337200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:120316200-120318600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:120316200-120318800	Enhancers	Stomach Mucosa	stomach
6	chr3:120316200-120323000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:120316200-120323800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:120316200-120335200	Weak transcription	Esophagus	oesophagus
9	chr3:120316400-120318000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:120316400-120318000	Genic enhancers	Brain Germinal Matrix	brain
11	chr3:120316400-120318400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:120316400-120318800	Genic enhancers	Fetal Lung	lung
13	chr3:120316400-120319800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:120316400-120320000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:120316600-120317600	Genic enhancers	Fetal Intestine Large	intestine
16	chr3:120316600-120317800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
17	chr3:120316600-120318000	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr3:120316600-120318000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:120316600-120318000	Genic enhancers	Brain Cingulate Gyrus	brain
20	chr3:120316600-120318200	Genic enhancers	Brain Inferior Temporal Lobe	brain
21	chr3:120316600-120318400	Genic enhancers	Liver	Liver
22	chr3:120316600-120318400	Genic enhancers	Fetal Brain Male	brain
23	chr3:120316600-120318600	Strong transcription	Fetal Muscle Trunk	muscle
24	chr3:120316600-120318800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:120316600-120318800	Strong transcription	Fetal Muscle Leg	muscle
26	chr3:120316600-120318800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
27	chr3:120316600-120319000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:120316600-120319200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr3:120316600-120321800	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:120316600-120322200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:120316600-120322200	Strong transcription	HSMM	muscle
32	chr3:120316600-120322400	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr3:120316600-120323600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:120316800-120317600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr3:120316800-120317600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:120316800-120317600	Strong transcription	Fetal Intestine Small	intestine
37	chr3:120316800-120317600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
38	chr3:120316800-120317600	Weak transcription	Hela-S3	cervix
39	chr3:120316800-120317800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:120316800-120317800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:120316800-120317800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:120316800-120317800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr3:120316800-120317800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:120316800-120317800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:120316800-120317800	Strong transcription	Fetal Stomach	stomach
46	chr3:120316800-120317800	Enhancers	Right Atrium	heart
47	chr3:120316800-120317800	Enhancers	Right Ventricle	heart
48	chr3:120316800-120318000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:120316800-120318000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:120316800-120318000	Strong transcription	Primary B cells from peripheral blood	blood

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