Variant report

Variant	rs1552776
Chromosome Location	chr8:19540306-19540307
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr8:19539778-19540389	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr8:19539623-19540360	MCF10A-Er-Src	breast:	n/a	n/a
3	GATA3	chr8:19540096-19540750	SH-SY5Y	brain:	n/a	chr8:19540311-19540328 chr8:19540320-19540329
4	FOS	chr8:19539888-19540379	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr8:19540011-19540590	Hela-S3	cervix:	n/a	n/a
6	STAT3	chr8:19539850-19540504	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr8:19538316-19541049	IMR90	lung:	n/a	n/a
8	POLR2A	chr8:19539605-19540431	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr8:19539698-19540451	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr8:19539936-19540445	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr8:19539843-19540447	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr8:19539566-19540417	MCF10A-Er-Src	breast:	n/a	n/a
13	GATA3	chr8:19540269-19540724	MCF-7	breast:	n/a	chr8:19540311-19540328 chr8:19540320-19540329
14	NR2F2	chr8:19540297-19540868	MCF-7	breast:	n/a	n/a
15	FOS	chr8:19539691-19540395	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr8:19539699-19540394	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr8:19539981-19540476	U87	brain:	n/a	n/a
18	CEBPB	chr8:19539966-19540528	IMR90	lung:	n/a	chr8:19540132-19540143
19	GATA2	chr8:19539931-19540976	SH-SY5Y	brain:	n/a	chr8:19540311-19540328 chr8:19540320-19540329
20	STAT3	chr8:19539884-19540435	MCF10A-Er-Src	breast:	n/a	n/a
21	RAD21	chr8:19539714-19540478	IMR90	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr8:19540272-19540322	HUVEC	blood vessel:	n/a
2	chr8:19540272-19540322	NHBE	bronchial:	n/a
3	chr8:19540272-19540322	HCPEpiC	choroid plexus:	n/a
4	chr8:19540272-19540322	NH-A	brain:	n/a
5	chr8:19540272-19540322	SK-N-MC	brain:	n/a
6	chr8:19540272-19540322	PrEC	prostate:	n/a
7	chr8:19540272-19540322	HAEpiC	amniotic membrane:	n/a
8	chr8:19540272-19540322	Caco-2	colon:	n/a
9	chr8:19540272-19540322	MCF10A-Er-Src	breast:	n/a
10	chr8:19540272-19540322	HEK293	kidney:	embryo
11	chr8:19540272-19540322	IMR90	lung:	fetal
12	chr8:19540272-19540322	HEEpiC	esophagus:	n/a
13	chr8:19540272-19540322	PANC-1	pancreas:	n/a
14	chr8:19540272-19540322	HRE	kidney:	n/a
15	chr8:19540272-19540322	GM19239	blood:	n/a
16	chr8:19540272-19540322	PFSK-1	brain:	n/a
17	chr8:19540272-19540322	Hela-S3	cervix:	n/a
18	chr8:19540272-19540322	LNCaP	prostate:	n/a
19	chr8:19540272-19540322	ovcar-3	ovarian:	n/a
20	chr8:19540272-19540322	H1-hESC	embryonic stem cell:	embryo
21	chr8:19540272-19540322	NB4	blood:	n/a
22	chr8:19540272-19540322	HRPEpiC	eye:	n/a
23	chr8:19540272-19540322	HPAEpiC	pulmonary alveolar:	n/a
24	chr8:19540272-19540322	T-47D	breast:	n/a
25	chr8:19540272-19540322	HRCEpiC	kidney:	n/a
26	chr8:19540272-19540322	GM12892	blood:	n/a
27	chr8:19540272-19540322	ECC-1	luminal epithelium:	n/a
28	chr8:19540272-19540322	A549	lung:	n/a
29	chr8:19540272-19540322	Hepatocyte	liver:	n/a
30	chr8:19540272-19540322	GM12878	blood:	n/a
31	chr8:19540272-19540322	HepG2	liver:	n/a
32	chr8:19540272-19540322	SK-N-SH_RA	brain:	n/a
33	chr8:19540272-19540322	SK-N-SH	brain:	n/a
34	chr8:19540272-19540322	HL-60	blood:	n/a
35	chr8:19540272-19540322	AG10803	skin:	n/a
36	chr8:19540272-19540322	Jurkat	blood:	n/a
37	chr8:19540272-19540322	NT2-D1	testis:	n/a
38	chr8:19540272-19540322	K562	blood:	n/a
39	chr8:19540272-19540322	AG04450	lung:	fetal
40	chr8:19540272-19540322	AoSMC	blood vessel:	n/a
41	chr8:19540272-19540322	HNPCEpiC	eye:	n/a
42	chr8:19540272-19540322	AG09319	gingival:	n/a
43	chr8:19540272-19540322	HCT-116	colon:	n/a
44	chr8:19540272-19540322	HCF	heart:	n/a
45	chr8:19540272-19540322	U87	brain:	n/a
46	chr8:19540272-19540322	CMK	blood:	n/a
47	chr8:19540272-19540322	ProgFib	skin:	n/a
48	chr8:19540272-19540322	HMEC	breast:	n/a
49	chr8:19540272-19540322	BJ	skin:	n/a
50	chr8:19540272-19540322	RPTEC	kidney:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:19535486..19538060-chr8:19539195..19541920,3	K562	blood:
2	chr8:19535666..19538060-chr8:19539355..19541920,2	K562	blood:

No data

Variant related genes	Relation type
CSGALNACT1	TF binding region
CSGALNACT1	CpG island
ENSG00000253270	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11204060	1.00[JPT][hapmap]
rs11778161	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11780937	1.00[JPT][hapmap]
rs11784031	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1552778	1.00[JPT][hapmap]
rs1552783	0.95[CEU][hapmap];0.87[YRI][hapmap];0.87[EUR][1000 genomes]
rs17409194	1.00[JPT][hapmap]
rs17481063	1.00[JPT][hapmap]
rs17481277	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17481361	0.95[CEU][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3735958	0.95[CEU][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7812740	1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7843349	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949636	chr8:18957705-19664732	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
2	nsv948861	chr8:19199688-19609029	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949304	chr8:19199688-19625912	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv890625	chr8:19368697-19799641	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv890627	chr8:19389865-19561997	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1021575	chr8:19430653-19623452	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh 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 lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1025271	chr8:19435147-19574969	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv6106	chr8:19499554-19544249	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1021731	chr8:19515149-19643313	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv890628	chr8:19527536-19540966	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv465602	chr8:19536015-19555398	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv610757	chr8:19536015-19555398	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv465603	chr8:19537084-19555398	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv465604	chr8:19537084-19555398	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv465606	chr8:19537084-19555398	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv465607	chr8:19537084-19555398	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv470203	chr8:19537084-19555398	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv610758	chr8:19537084-19555398	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1552776	CSGALNACT1	cis	Whole Blood	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:19536200-19540800	Enhancers	Pancreas	Pancrea
2	chr8:19536400-19543600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr8:19537600-19541000	Genic enhancers	A549	lung
4	chr8:19538400-19541200	Enhancers	Fetal Heart	heart
5	chr8:19538400-19541400	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr8:19538600-19540600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr8:19538600-19541000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr8:19538800-19540400	Enhancers	Esophagus	oesophagus
9	chr8:19538800-19540600	Enhancers	Fetal Thymus	thymus
10	chr8:19538800-19540600	Enhancers	Gastric	stomach
11	chr8:19538800-19540800	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr8:19538800-19540800	Enhancers	Lung	lung
13	chr8:19538800-19541000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr8:19538800-19541000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr8:19538800-19541000	Enhancers	HMEC	breast
16	chr8:19539000-19540400	Enhancers	Stomach Mucosa	stomach
17	chr8:19539000-19540600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr8:19539000-19540600	Enhancers	Thymus	Thymus
19	chr8:19539000-19540800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr8:19539000-19540800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr8:19539000-19540800	Enhancers	Ovary	ovary
22	chr8:19539000-19541000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr8:19539000-19541600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr8:19539200-19540400	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr8:19539200-19540400	Enhancers	Aorta	Aorta
26	chr8:19539200-19540400	Enhancers	Fetal Muscle Trunk	muscle
27	chr8:19539200-19540600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr8:19539200-19540600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr8:19539200-19540600	Enhancers	NHLF	lung
30	chr8:19539200-19541000	Enhancers	Fetal Brain Female	brain
31	chr8:19539200-19542200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr8:19539400-19540600	Enhancers	Brain Angular Gyrus	brain
33	chr8:19539400-19540800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr8:19539400-19540800	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr8:19539400-19540800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr8:19539400-19552000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr8:19539600-19540800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr8:19539600-19540800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr8:19539600-19541000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr8:19539600-19541000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr8:19539600-19541200	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr8:19539600-19541400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr8:19539600-19548200	Weak transcription	Brain Anterior Caudate	brain
44	chr8:19539800-19540400	Enhancers	Brain Germinal Matrix	brain
45	chr8:19539800-19540600	Flanking Active TSS	Placenta	Placenta
46	chr8:19539800-19540600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr8:19539800-19540600	Flanking Active TSS	NH-A	brain
48	chr8:19539800-19540800	Flanking Active TSS	Left Ventricle	heart
49	chr8:19540000-19540400	Enhancers	Adipose Nuclei	Adipose
50	chr8:19540000-19540400	Flanking Active TSS	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links