Variant report

Variant	rs3825078
Chromosome Location	chr12:58089413-58089414
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58086909..58089805-chr12:58175888..58177930,2	K562	blood:
2	chr12:58086950..58089833-chr12:58113163..58115231,2	K562	blood:
3	chr12:58087963..58090015-chr12:58135422..58139186,3	K562	blood:
4	chr12:58007718..58010411-chr12:58087376..58090012,2	MCF-7	breast:
5	chr12:58088175..58090012-chr12:58107431..58109845,2	K562	blood:
6	chr12:57913089..57916136-chr12:58086816..58089656,3	MCF-7	breast:
7	chr12:57983190..57986031-chr12:58086563..58089648,3	K562	blood:

Variant related genes	Relation type
ENSG00000135439	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000224713	Chromatin interaction
ENSG00000240771	Chromatin interaction
ENSG00000123297	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000166987	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10082911	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083154	0.87[CEU][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs10783836	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10783842	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783843	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783844	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1082502	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1082503	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10876993	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs10876994	0.87[CHB][hapmap]
rs10877001	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877006	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877007	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877008	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1092472	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172277	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172304	0.85[AFR][1000 genomes]
rs11172306	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12302351	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12302451	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12314562	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12316021	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12809742	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12813384	0.87[ASN][1000 genomes]
rs1585781	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1628552	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1629032	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1633360	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1633361	0.88[ASN][1000 genomes]
rs1678504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678505	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1678511	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678512	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1678513	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1678515	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1678516	0.92[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1678520	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1678522	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1678527	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1678528	0.88[ASN][1000 genomes]
rs1678529	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1678530	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678531	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678532	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1678534	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1678539	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1678540	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1689584	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1689585	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1689586	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1689592	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1689594	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1689595	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1689596	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1689597	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1689600	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1689601	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1689604	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1696466	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1871417	0.87[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs2277322	0.82[JPT][hapmap]
rs238516	0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2619441	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619466	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2640629	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2640630	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2640631	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2928053	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2928054	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2928055	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2928061	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2928062	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928064	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760164	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4760165	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs701006	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs703832	0.84[EUR][1000 genomes]
rs7136269	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7314152	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs774887	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs774888	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs774890	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs774891	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7976852	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7979246	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799575	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs810204	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv508676	chr12:58045136-58098538	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
4	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3825078	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs3825078	SLC26A10	cis	Heart Left Ventricle	GTEx
rs3825078	TSFM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58088800-58089600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr12:58088800-58089600	Enhancers	Fetal Intestine Large	intestine
3	chr12:58088800-58089600	Weak transcription	Psoas Muscle	Psoas
4	chr12:58088800-58090200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
5	chr12:58088800-58090600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:58088800-58093400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:58088800-58097800	Strong transcription	Fetal Muscle Trunk	muscle
8	chr12:58088800-58099400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:58088800-58099400	Weak transcription	Small Intestine	intestine
10	chr12:58089000-58089600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:58089000-58089600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:58089000-58089600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:58089000-58089600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:58089000-58089600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:58089000-58089600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:58089000-58089600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr12:58089000-58089600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr12:58089000-58089600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:58089000-58089600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:58089000-58089600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:58089000-58089600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:58089000-58089600	Weak transcription	Brain Substantia Nigra	brain
23	chr12:58089000-58089600	Weak transcription	Fetal Kidney	kidney
24	chr12:58089000-58089600	Weak transcription	Placenta	Placenta
25	chr12:58089000-58089600	Weak transcription	Gastric	stomach
26	chr12:58089000-58089600	Weak transcription	Left Ventricle	heart
27	chr12:58089000-58089600	Weak transcription	Pancreas	Pancrea
28	chr12:58089000-58089600	Weak transcription	Thymus	Thymus
29	chr12:58089000-58089600	Enhancers	Hela-S3	cervix
30	chr12:58089000-58089600	Weak transcription	HUVEC	blood vessel
31	chr12:58089000-58089800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:58089000-58089800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:58089000-58089800	Enhancers	Fetal Intestine Small	intestine
34	chr12:58089000-58089800	Weak transcription	Right Ventricle	heart
35	chr12:58089000-58089800	Genic enhancers	Dnd41	blood
36	chr12:58089000-58089800	Genic enhancers	K562	blood
37	chr12:58089000-58089800	Weak transcription	NHDF-Ad	bronchial
38	chr12:58089000-58090000	Weak transcription	Esophagus	oesophagus
39	chr12:58089000-58090800	Weak transcription	NH-A	brain
40	chr12:58089000-58091000	Weak transcription	Aorta	Aorta
41	chr12:58089000-58091000	Weak transcription	Fetal Brain Male	brain
42	chr12:58089000-58092000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:58089000-58092200	Strong transcription	Rectal Smooth Muscle	rectum
44	chr12:58089000-58092800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:58089000-58092800	Strong transcription	Fetal Lung	lung
46	chr12:58089000-58092800	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr12:58089000-58094000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:58089000-58094200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:58089000-58095800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr12:58089000-58097000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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