Variant report

Variant	rs277620
Chromosome Location	chr3:100057269-100057270
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	chr3:100057204-100057690	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:100056720-100057772	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:100057219-100057289	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:100055925..100057917-chr3:100076174..100079116,2	MCF-7	breast:
2	chr3:100051539..100055958-chr3:100056037..100061247,9	MCF-7	breast:
3	chr3:100056838..100058599-chr3:100119834..100121558,2	MCF-7	breast:

Variant related genes	Relation type
NIT2	TF binding region
ENSG00000114021	Chromatin interaction
ENSG00000206535	Chromatin interaction
ENSG00000154174	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1045206	0.97[YRI][hapmap];0.82[AFR][1000 genomes]
rs10936180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1123578	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1214375	0.93[YRI][hapmap]
rs1214380	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1214381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1228184	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1530283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs166747	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277622	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277623	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277626	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277628	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277629	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277630	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs277635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277644	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277651	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs372438	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3772692	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3806615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs392066	1.00[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs395399	0.83[AFR][1000 genomes]
rs402870	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs413425	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs431069	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs432715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6791102	0.88[ASN][1000 genomes]
rs6794955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7616634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7641630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv3387925	chr3:100056362-100059860	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054000-100065000	Weak transcription	Spleen	Spleen
2	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:100054400-100067600	Weak transcription	Psoas Muscle	Psoas
4	chr3:100054600-100057400	Weak transcription	Primary T cells from cord blood	blood
5	chr3:100054600-100058000	Weak transcription	Fetal Brain Male	brain
6	chr3:100054600-100058000	Weak transcription	Fetal Brain Female	brain
7	chr3:100054600-100058200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:100054600-100058400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:100054600-100058600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:100054600-100058600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:100054600-100058800	Weak transcription	Aorta	Aorta
12	chr3:100054600-100059400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:100054600-100059800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:100054600-100060200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:100054600-100063000	Weak transcription	Brain Substantia Nigra	brain
16	chr3:100054600-100064200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:100054600-100064400	Weak transcription	Thymus	Thymus
18	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr3:100054800-100057400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:100054800-100057400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr3:100054800-100057600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:100054800-100057600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:100054800-100057600	Weak transcription	Adipose Nuclei	Adipose
24	chr3:100054800-100057600	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:100054800-100057600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:100054800-100057800	Enhancers	Liver	Liver
27	chr3:100054800-100057800	Weak transcription	Gastric	stomach
28	chr3:100054800-100057800	Weak transcription	Ovary	ovary
29	chr3:100054800-100057800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:100054800-100057800	Weak transcription	NHDF-Ad	bronchial
31	chr3:100054800-100058000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr3:100054800-100058000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr3:100054800-100058000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:100054800-100058000	Weak transcription	Fetal Thymus	thymus
35	chr3:100054800-100058000	Weak transcription	Left Ventricle	heart
36	chr3:100054800-100058000	Weak transcription	Lung	lung
37	chr3:100054800-100058000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:100054800-100058000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:100054800-100058000	Weak transcription	HSMMtube	muscle
40	chr3:100054800-100058400	Weak transcription	NH-A	brain
41	chr3:100054800-100058600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:100054800-100058600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:100054800-100058800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:100054800-100058800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:100054800-100059400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr3:100054800-100059400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr3:100054800-100060000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:100054800-100060000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:100054800-100060200	Weak transcription	Right Ventricle	heart
50	chr3:100054800-100060600	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links