Variant report

Variant	rs3803025
Chromosome Location	chr12:49084434-49084435
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49083038..49084823-chr12:49212484..49215023,2	MCF-7	breast:
2	chr12:49081356..49082903-chr12:49083165..49085083,2	MCF-7	breast:
3	chr12:48744161..48745833-chr12:49082772..49084954,2	MCF-7	breast:
4	chr12:49072887..49077758-chr12:49080125..49086735,20	MCF-7	breast:
5	chr12:49079132..49081728-chr12:49082778..49085110,2	K562	blood:
6	chr12:49082621..49084947-chr12:49105438..49107834,2	K562	blood:
7	chr12:49081164..49084548-chr12:49085177..49089897,6	K562	blood:
8	chr12:49079308..49081077-chr12:49084026..49086019,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCNT1-1	chr12:49082247-49086290	NONHSAT028017

No data

Variant related genes	Relation type
ENSG00000167528	Chromatin interaction
ENSG00000257735	Chromatin interaction
ENSG00000139620	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000129315	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10747554	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10783273	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10783274	0.85[ASN][1000 genomes]
rs10783275	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783277	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs10783278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783281	0.87[EUR][1000 genomes]
rs10875849	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs10875850	0.90[ASN][1000 genomes]
rs10875852	0.95[ASN][1000 genomes]
rs10875853	0.95[ASN][1000 genomes]
rs10875861	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10875862	0.95[ASN][1000 genomes]
rs1110432	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168657	0.88[ASN][1000 genomes]
rs11168665	0.95[ASN][1000 genomes]
rs11168674	0.93[ASN][1000 genomes]
rs11168697	0.87[ASN][1000 genomes]
rs11168698	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11168702	0.81[JPT][hapmap]
rs12299955	0.87[ASN][1000 genomes]
rs12426435	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1316514	0.93[ASN][1000 genomes]
rs1863541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1895995	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2114320	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2162317	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2277365	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2277366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2409085	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2898087	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3209584	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35717253	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3741628	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3741629	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3741630	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3741632	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3943899	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4113946	0.90[ASN][1000 genomes]
rs4500528	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4760735	0.90[ASN][1000 genomes]
rs4760737	0.91[ASN][1000 genomes]
rs4760739	0.90[ASN][1000 genomes]
rs4760740	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580689	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580690	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580692	0.83[EUR][1000 genomes]
rs6580693	0.91[EUR][1000 genomes]
rs7133756	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap]
rs7136021	0.81[ASN][1000 genomes]
rs7138190	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7138930	0.88[CEU][hapmap];0.84[TSI][hapmap]
rs7139236	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299276	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7304711	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7305907	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7306604	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7308699	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7314665	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7954446	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7954548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs7964546	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7966065	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7973824	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7974151	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7974625	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7975030	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7975821	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9332441	0.95[ASN][1000 genomes]
rs9634241	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9634242	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9634262	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3803025	ADCY6	cis	parietal	SCAN
rs3803025	SNORA2B	cis	cerebellum	SCAN
rs3803025	FAM186B	cis	cerebellum	SCAN
rs3803025	ZNF641	cis	cerebellum	SCAN
rs3803025	WNT10B	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49076000-49087000	Weak transcription	Stomach Mucosa	stomach
2	chr12:49076600-49084800	Weak transcription	Colonic Mucosa	Colon
3	chr12:49076600-49085600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:49076600-49086400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:49076600-49086400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:49076600-49086400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:49076600-49086400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:49076600-49086600	Weak transcription	Fetal Kidney	kidney
9	chr12:49076600-49086800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:49076600-49086800	Weak transcription	Aorta	Aorta
11	chr12:49076600-49086800	Weak transcription	Esophagus	oesophagus
12	chr12:49076600-49086800	Weak transcription	Gastric	stomach
13	chr12:49076600-49086800	Weak transcription	Ovary	ovary
14	chr12:49076600-49086800	Weak transcription	Pancreas	Pancrea
15	chr12:49076600-49086800	Weak transcription	Spleen	Spleen
16	chr12:49076600-49096400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:49076600-49109000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:49076800-49085400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:49076800-49085800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:49076800-49085800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr12:49076800-49086800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr12:49076800-49086800	Weak transcription	Fetal Intestine Small	intestine
23	chr12:49077000-49084800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:49077000-49085800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:49077000-49085800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:49077000-49086800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:49077000-49087000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:49077200-49085600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:49077200-49085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:49077200-49086400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr12:49077200-49087000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:49080800-49097400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:49081000-49086800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:49081000-49097200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:49081000-49101000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:49081200-49090800	Strong transcription	HSMM	muscle
37	chr12:49081200-49093600	Strong transcription	NH-A	brain
38	chr12:49081400-49090400	Strong transcription	Brain Anterior Caudate	brain
39	chr12:49081400-49104000	Strong transcription	Hela-S3	cervix
40	chr12:49081600-49090000	Strong transcription	Primary hematopoietic stem cells	blood
41	chr12:49081600-49090200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:49081600-49090600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:49081600-49092400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr12:49081600-49093600	Strong transcription	Osteobl	bone
45	chr12:49081600-49095000	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr12:49081600-49097400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:49081600-49099800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr12:49081600-49103800	Strong transcription	Dnd41	blood
49	chr12:49081600-49107200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:49081600-49107600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links