Variant report

Variant	rs277629
Chromosome Location	chr3:100054646-100054647
allele	A/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	HDAC2	chr3:100054355-100054663	K562	blood:	n/a	n/a
2	POLR2A	chr3:100053973-100054744	K562	blood:	n/a	n/a
3	RCOR1	chr3:100053387-100054933	K562	blood:	n/a	n/a
4	POLR2A	chr3:100052685-100054939	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:100053313-100055020	K562	blood:	n/a	n/a
6	POLR2A	chr3:100053059-100054674	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr3:100054502-100054678	MCF-7	breast:	n/a	n/a
8	MXI1	chr3:100052857-100054783	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr3:100053112-100054666	GM12878	blood:	n/a	n/a
10	SPI1	chr3:100054225-100054704	HL-60	blood:	n/a	chr3:100054380-100054389 chr3:100054504-100054511
11	POLR2A	chr3:100054267-100054700	GM12878	blood:	n/a	n/a
12	MAX	chr3:100054295-100054794	K562	blood:	n/a	chr3:100054520-100054529
13	POLR2A	chr3:100053236-100054653	GM12891	blood:	n/a	n/a
14	POLR2A	chr3:100053276-100054688	HL-60	blood:	n/a	n/a
15	TBP	chr3:100053209-100054712	K562	blood:	n/a	n/a
16	POLR2A	chr3:100053155-100055087	GM12891	blood:	n/a	n/a
17	POLR2A	chr3:100054204-100054668	GM12891	blood:	n/a	n/a
18	POLR2A	chr3:100054389-100054694	MCF-7	breast:	n/a	n/a
19	ATF1	chr3:100054299-100054736	K562	blood:	n/a	n/a
20	MAX	chr3:100053086-100054743	NB4	blood:	n/a	chr3:100054520-100054529
21	POLR2A	chr3:100053228-100054809	GM19193	blood:	n/a	n/a
22	YY1	chr3:100054276-100054696	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:100053130-100054871	GM12892	blood:	n/a	n/a
24	HEY1	chr3:100053398-100054694	K562	blood:	n/a	n/a
25	POLR2A	chr3:100054147-100054756	HL-60	blood:	n/a	n/a
26	POLR2A	chr3:100053083-100054826	GM12892	blood:	n/a	n/a
27	CBX3	chr3:100054244-100054908	K562	blood:	n/a	n/a
28	POLR2A	chr3:100053142-100054796	GM12878	blood:	n/a	n/a
29	POLR2A	chr3:100053176-100054783	GM12891	blood:	n/a	n/a
30	E2F6	chr3:100054210-100054757	K562	blood:	n/a	chr3:100054539-100054550
31	POLR2A	chr3:100053052-100055002	HepG2	liver:	n/a	n/a
32	JUND	chr3:100053384-100054685	K562	blood:	n/a	n/a
33	MAX	chr3:100053109-100054670	A549	lung:	n/a	chr3:100054520-100054529
34	POLR2A	chr3:100053194-100054865	Hela-S3	cervix:	n/a	n/a
35	MAX	chr3:100053314-100054791	K562	blood:	n/a	chr3:100054520-100054529
36	MYC	chr3:100053404-100054894	K562	blood:	n/a	chr3:100054520-100054529
37	MAZ	chr3:100053233-100054696	K562	blood:	n/a	chr3:100054520-100054529
38	POLR2A	chr3:100053242-100054674	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:100053198-100054708	GM19099	blood:	n/a	n/a
40	TAL1	chr3:100054269-100054671	K562	blood:	n/a	n/a
41	POLR2A	chr3:100053273-100054900	MCF10A-Er-Src	breast:	n/a	n/a
42	YY1	chr3:100054295-100054668	K562	blood:	n/a	n/a
43	POLR2A	chr3:100054384-100054714	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr3:100054211-100054657	K562	blood:	n/a	n/a
45	MYC	chr3:100053105-100054661	NB4	blood:	n/a	chr3:100054520-100054529
46	POLR2A	chr3:100053073-100054731	Raji	blood:	n/a	n/a
47	POLR2A	chr3:100053260-100054742	GM12892	blood:	n/a	n/a
48	POLR2A	chr3:100053173-100054739	NB4	blood:	n/a	n/a
49	POLR2A	chr3:100054241-100054713	K562	blood:	n/a	n/a
50	POLR2A	chr3:100054259-100054850	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:100052434..100055247-chr3:100118351..100122265,5	K562	blood:
2	chr3:100051539..100055958-chr3:100056037..100061247,9	MCF-7	breast:
3	chr3:100052074..100055881-chr3:100116822..100121530,5	MCF-7	breast:

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

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1045206	0.94[YRI][hapmap]
rs10936180	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1123578	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1214375	0.90[YRI][hapmap]
rs1214380	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1214381	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1228184	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12495001	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs1530283	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs166747	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277620	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]
rs277622	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277623	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277626	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277628	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs277630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277633	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277634	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277635	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277638	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277642	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277644	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277651	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs372438	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772692	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3806615	0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs392066	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs402870	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs413425	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs431069	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs432715	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6780662	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6791102	0.87[ASN][1000 genomes]
rs6794955	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7616634	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7641630	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[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	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100052800-100054800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:100052800-100054800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:100053400-100054800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr3:100053400-100054800	Active TSS	Osteobl	bone
5	chr3:100054000-100054800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:100054000-100054800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr3:100054000-100054800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr3:100054000-100054800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:100054000-100054800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr3:100054000-100054800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:100054000-100054800	Flanking Active TSS	Liver	Liver
12	chr3:100054000-100054800	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr3:100054000-100054800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr3:100054000-100055000	Flanking Active TSS	Dnd41	blood
15	chr3:100054000-100065000	Weak transcription	Spleen	Spleen
16	chr3:100054200-100054800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:100054200-100054800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:100054200-100054800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:100054200-100054800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:100054200-100054800	Enhancers	Esophagus	oesophagus
21	chr3:100054200-100054800	Enhancers	Gastric	stomach
22	chr3:100054200-100054800	Enhancers	Left Ventricle	heart
23	chr3:100054200-100054800	Enhancers	Lung	lung
24	chr3:100054200-100054800	Enhancers	Placenta Amnion	Placenta Amnion
25	chr3:100054200-100054800	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr3:100054200-100054800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr3:100054200-100054800	Enhancers	Small Intestine	intestine
28	chr3:100054200-100054800	Flanking Active TSS	Hela-S3	cervix
29	chr3:100054200-100054800	Flanking Active TSS	HMEC	breast
30	chr3:100054200-100054800	Flanking Active TSS	K562	blood
31	chr3:100054200-100055000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:100054200-100055000	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr3:100054200-100055000	Enhancers	Fetal Heart	heart
34	chr3:100054200-100055200	Flanking Active TSS	Fetal Intestine Large	intestine
35	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:100054400-100054800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:100054400-100054800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:100054400-100054800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:100054400-100054800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:100054400-100054800	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr3:100054400-100054800	Enhancers	Primary B cells from cord blood	blood
42	chr3:100054400-100054800	Enhancers	Primary B cells from peripheral blood	blood
43	chr3:100054400-100054800	Enhancers	Primary T cells fromperipheralblood	blood
44	chr3:100054400-100054800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr3:100054400-100054800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr3:100054400-100054800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr3:100054400-100054800	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr3:100054400-100054800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr3:100054400-100054800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:100054400-100054800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links