Variant report

Variant	rs9839819
Chromosome Location	chr3:133931135-133931136
allele	A/C
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	CTCF	chr3:133931100-133931250	GM12875	blood:	n/a	n/a
2	RAD21	chr3:133930515-133931295	SK-N-SH	brain:	n/a	chr3:133930855-133930869
3	CTCF	chr3:133931060-133931210	GM12873	blood:	n/a	n/a
4	CTCF	chr3:133931118-133931188	GM10266	blood:	n/a	n/a
5	CTCF	chr3:133930633-133931164	MCF-7	breast:	n/a	chr3:133930853-133930871
6	SMC3	chr3:133929883-133931301	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr3:133931100-133931250	BJ	skin:	n/a	n/a
8	POLR2A	chr3:133931066-133931276	A549	lung:	n/a	n/a
9	CTCF	chr3:133931100-133931250	HRPEpiC	eye:	n/a	n/a
10	CTCF	chr3:133930456-133932489	SK-N-SH	brain:	n/a	chr3:133931927-133931940 chr3:133931924-133931942 chr3:133930853-133930871 chr3:133931925-133931941 chr3:133931929-133931939 chr3:133931926-133931947 chr3:133931927-133931936 chr3:133931924-133931937
11	CTCF	chr3:133930486-133931145	HCT-116	colon:	n/a	chr3:133930853-133930871
12	NFYA	chr3:133930904-133931155	GM12878	blood:	n/a	chr3:133931125-133931140 chr3:133931127-133931137 chr3:133931125-133931140
13	RAD21	chr3:133930522-133931181	HCT-116	colon:	n/a	chr3:133930855-133930869
14	CTCF	chr3:133930436-133931235	A549	lung:	n/a	chr3:133930853-133930871

No.	Distal block	Cell Line	Cell type
1	chr3:133649153..133649802-chr3:133930619..133931350,4	MCF-7	breast:
2	chr3:133682859..133683724-chr3:133930459..133931279,2	MCF-7	breast:
3	chr3:133929438..133933511-chr3:133934266..133936727,4	K562	blood:
4	chr3:133916172..133917171-chr3:133930199..133931384,7	MCF-7	breast:
5	chr3:133915566..133917732-chr3:133929901..133931438,2	MCF-7	breast:
6	chr3:133931051..133933200-chr3:134201381..134203725,2	MCF-7	breast:
7	chr3:133650886..133653497-chr3:133930540..133932971,2	MCF-7	breast:
8	chr3:133930775..133933152-chr3:133968044..133970596,3	MCF-7	breast:
9	chr3:133648968..133649874-chr3:133930231..133931413,8	MCF-7	breast:
10	chr3:133929711..133931992-chr3:134027528..134029983,2	MCF-7	breast:
11	chr3:133924472..133926477-chr3:133931064..133932575,2	K562	blood:
12	chr3:133916838..133918592-chr3:133930697..133932431,2	MCF-7	breast:
13	chr3:133930920..133932595-chr3:134018162..134020016,12	MCF-7	breast:

Variant related genes	Relation type
RYK	TF binding region
ENSG00000163785	Chromatin interaction
ENSG00000129055	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10804630	0.88[GIH][hapmap];0.93[MEX][hapmap]
rs10935104	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs1131262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707763	0.88[ASN][1000 genomes]
rs11915143	0.88[ASN][1000 genomes]
rs35322473	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3890774	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4072180	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4324466	0.89[ASN][1000 genomes]
rs4682664	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682666	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682669	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55689708	0.81[ASN][1000 genomes]
rs56073423	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439465	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439466	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6650893	0.88[ASN][1000 genomes]
rs6762690	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6776502	0.92[CEU][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6780295	0.88[ASN][1000 genomes]
rs6800143	0.89[ASN][1000 genomes]
rs6808085	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]
rs7355922	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7609611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9283588	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9812461	0.85[ASN][1000 genomes]
rs9818714	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9823873	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9825808	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827728	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9832732	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[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]
rs9853568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9856298	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9856792	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858069	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858450	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9858707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers 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	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9839819	DBR1	cis	parietal	SCAN
rs9839819	PIK3CB	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133874600-133933600	Weak transcription	Colonic Mucosa	Colon
2	chr3:133877600-133935200	Weak transcription	Psoas Muscle	Psoas
3	chr3:133877800-133950200	Weak transcription	Small Intestine	intestine
4	chr3:133894800-133935200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:133894800-133946800	Weak transcription	Pancreas	Pancrea
6	chr3:133895000-133950000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:133895000-133950200	Weak transcription	Gastric	stomach
8	chr3:133895600-133942800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr3:133909200-133943000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:133919000-133950600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:133919400-133943000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:133919800-133940200	Weak transcription	Esophagus	oesophagus
13	chr3:133920000-133940200	Weak transcription	Fetal Intestine Small	intestine
14	chr3:133920200-133934000	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:133920200-133938200	Weak transcription	Fetal Brain Male	brain
16	chr3:133920400-133938600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:133920600-133932000	Weak transcription	Brain Anterior Caudate	brain
18	chr3:133920600-133938400	Weak transcription	HSMMtube	muscle
19	chr3:133920600-133940600	Weak transcription	A549	lung
20	chr3:133920800-133931800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:133920800-133932000	Weak transcription	Ovary	ovary
22	chr3:133920800-133940600	Weak transcription	Thymus	Thymus
23	chr3:133920800-133950200	Weak transcription	Aorta	Aorta
24	chr3:133920800-133950200	Weak transcription	Spleen	Spleen
25	chr3:133920800-133950600	Weak transcription	Hela-S3	cervix
26	chr3:133921200-133931800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:133921400-133934600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:133921600-133932000	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:133921600-133937200	Weak transcription	Fetal Stomach	stomach
30	chr3:133921600-133941800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:133921800-133931800	Weak transcription	Brain Angular Gyrus	brain
32	chr3:133921800-133943000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:133923600-133931200	Strong transcription	Primary T cells from cord blood	blood
34	chr3:133923800-133934200	Strong transcription	Primary B cells from cord blood	blood
35	chr3:133924600-133941800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:133926000-133931400	Strong transcription	Dnd41	blood
37	chr3:133927000-133932400	Enhancers	Fetal Heart	heart
38	chr3:133928000-133932000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:133928600-133949400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr3:133929600-133931400	Genic enhancers	NHEK	skin
41	chr3:133929800-133931200	Strong transcription	Fetal Muscle Leg	muscle
42	chr3:133930000-133931800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:133930000-133933400	Enhancers	HMEC	breast
44	chr3:133930000-133934200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:133930000-133935800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:133930000-133942400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr3:133930000-133950000	Weak transcription	NHDF-Ad	bronchial
48	chr3:133930000-133950400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:133930000-133954600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr3:133930200-133931200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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