Variant report

Variant	rs12546960
Chromosome Location	chr8:103910513-103910514
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	FOXA1	chr8:103910196-103910675	T-47D	breast:	n/a	n/a
2	EP300	chr8:103910324-103910610	GM12878	blood:	n/a	n/a
3	SPI1	chr8:103910423-103910882	HL-60	blood:	n/a	chr8:103910603-103910616 chr8:103910602-103910615 chr8:103910604-103910613
4	TCF7L2	chr8:103910084-103910710	PANC-1	pancreas:	n/a	chr8:103910381-103910388
5	MAX	chr8:103910140-103910866	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr8:103910229-103911009	Hela-S3	cervix:	n/a	chr8:103910842-103910855
7	SPI1	chr8:103910424-103910744	GM12891	blood:	n/a	chr8:103910603-103910616 chr8:103910602-103910615 chr8:103910604-103910613
8	STAT3	chr8:103910268-103910662	Hela-S3	cervix:	n/a	n/a
9	USF2	chr8:103910266-103910851	Hela-S3	cervix:	n/a	n/a
10	FOXA1	chr8:103910196-103910578	T-47D	breast:	n/a	n/a
11	RAD21	chr8:103910276-103910763	Hela-S3	cervix:	n/a	n/a
12	GTF2F1	chr8:103910083-103910773	Hela-S3	cervix:	n/a	n/a
13	GATA3	chr8:103909918-103910770	T-47D	breast:	n/a	chr8:103910139-103910160 chr8:103910144-103910154 chr8:103910144-103910153 chr8:103910135-103910152
14	GATA3	chr8:103910042-103910677	T-47D	breast:	n/a	chr8:103910139-103910160 chr8:103910144-103910154 chr8:103910144-103910153 chr8:103910135-103910152
15	POLR2A	chr8:103910273-103910541	K562	blood:	n/a	n/a
16	POLR2A	chr8:103910387-103910751	Hela-S3	cervix:	n/a	n/a
17	TBP	chr8:103910257-103910697	Hela-S3	cervix:	n/a	n/a
18	SMC3	chr8:103910300-103910784	Hela-S3	cervix:	n/a	n/a
19	SPI1	chr8:103910439-103910796	HL-60	blood:	n/a	chr8:103910603-103910616 chr8:103910602-103910615 chr8:103910604-103910613
20	EP300	chr8:103910242-103910831	Hela-S3	cervix:	n/a	chr8:103910646-103910653
21	MAX	chr8:103910310-103910829	Hela-S3	cervix:	n/a	n/a
22	TCF7L2	chr8:103910094-103910711	Hela-S3	cervix:	n/a	chr8:103910381-103910388

No.	Distal block	Cell Line	Cell type
1	chr8:103909625..103914681-chr8:103915019..103918768,8	MCF-7	breast:
2	chr8:103893102..103894642-chr8:103909185..103910728,2	MCF-7	breast:
3	chr8:103907713..103911822-chr8:103912722..103917770,5	MCF-7	breast:
4	chr8:103874983..103877501-chr8:103909403..103912170,5	MCF-7	breast:

Variant related genes	Relation type
AZIN1	TF binding region
ENSG00000253320	Chromatin interaction
ENSG00000155096	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12544232	0.86[AMR][1000 genomes]
rs12546479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12546636	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12547652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12548745	1.00[CHB][hapmap]
rs12549011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12549073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12550185	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533182	1.00[CHB][hapmap]
rs17197341	0.89[AMR][1000 genomes]
rs17197736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17198079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17775390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2137339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2388369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2388370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734673	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734676	0.86[AMR][1000 genomes]
rs4734678	0.86[AMR][1000 genomes]
rs4734680	1.00[CHB][hapmap]
rs56854051	0.84[AMR][1000 genomes]
rs62522573	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62522576	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522623	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62522626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62526529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62526533	0.83[AMR][1000 genomes]
rs62526534	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1021898	chr8:103767324-103922482	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103879200-103922000	Weak transcription	Fetal Intestine Small	intestine
2	chr8:103894200-103914600	Weak transcription	Fetal Lung	lung
3	chr8:103896400-103911200	Weak transcription	Primary T cells from cord blood	blood
4	chr8:103905200-103910800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr8:103905400-103910800	Enhancers	Placenta	Placenta
6	chr8:103907000-103910600	Weak transcription	HSMM	muscle
7	chr8:103907000-103911600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr8:103907200-103912800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr8:103907400-103910600	Weak transcription	Right Ventricle	heart
10	chr8:103907400-103910800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr8:103907400-103910800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr8:103907400-103911200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr8:103907400-103915000	Weak transcription	Fetal Stomach	stomach
14	chr8:103907600-103910600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr8:103907600-103922600	Weak transcription	Brain Germinal Matrix	brain
16	chr8:103907800-103910600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:103907800-103911000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr8:103907800-103922000	Weak transcription	Fetal Brain Female	brain
19	chr8:103907800-103922600	Weak transcription	Gastric	stomach
20	chr8:103908000-103913200	Weak transcription	Spleen	Spleen
21	chr8:103908400-103910800	Enhancers	Rectal Smooth Muscle	rectum
22	chr8:103908600-103910800	Enhancers	Primary B cells from cord blood	blood
23	chr8:103908600-103911200	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr8:103908800-103911200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr8:103908800-103913000	Enhancers	Fetal Muscle Leg	muscle
26	chr8:103909000-103911800	Enhancers	Right Atrium	heart
27	chr8:103909000-103913400	Enhancers	Psoas Muscle	Psoas
28	chr8:103909200-103910600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr8:103909200-103911800	Enhancers	Left Ventricle	heart
30	chr8:103909200-103918200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr8:103909400-103910800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr8:103909400-103918600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr8:103910000-103910600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr8:103910000-103910800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr8:103910000-103910800	Enhancers	Stomach Mucosa	stomach
36	chr8:103910000-103910800	Enhancers	Dnd41	blood
37	chr8:103910000-103911000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr8:103910000-103911000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr8:103910000-103911000	Enhancers	Brain Anterior Caudate	brain
40	chr8:103910000-103911000	Enhancers	Colon Smooth Muscle	Colon
41	chr8:103910000-103911000	Enhancers	Stomach Smooth Muscle	stomach
42	chr8:103910000-103911200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr8:103910000-103911200	Enhancers	Liver	Liver
44	chr8:103910000-103911200	Enhancers	Duodenum Mucosa	Duodenum
45	chr8:103910000-103911200	Enhancers	Small Intestine	intestine
46	chr8:103910000-103911200	Flanking Active TSS	Hela-S3	cervix
47	chr8:103910000-103911400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr8:103910000-103911400	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr8:103910000-103911400	Enhancers	Brain Substantia Nigra	brain
50	chr8:103910000-103911600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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