Variant report

Variant	rs3886003
Chromosome Location	chr8:125513322-125513323
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125504143..125506439-chr8:125511671..125514041,2	K562	blood:
2	chr8:125507259..125508866-chr8:125511438..125514054,2	MCF-7	breast:
3	chr8:125512614..125515579-chr8:125518268..125520554,3	K562	blood:
4	chr8:125507542..125509103-chr8:125511076..125513358,2	K562	blood:
5	chr8:125511432..125513995-chr8:125518857..125520463,2	MCF-7	breast:
6	chr8:125508019..125510781-chr8:125511010..125514154,3	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10091243	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10092569	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10106292	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11987932	0.82[EUR][1000 genomes]
rs11991829	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12542293	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12548235	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28725399	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3812474	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3812475	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4128468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4269525	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4269526	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4870901	0.82[AMR][1000 genomes]
rs4871498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6470245	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6982197	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6984985	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987343	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs6993926	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7001480	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7005393	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7007115	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7009290	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7010411	0.91[JPT][hapmap]
rs7013683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7812331	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7812911	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7825599	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7827791	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7830506	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3886003	TRMT12	cis	Whole Blood	GTEx
rs3886003	TRMT12	cis	uninvolved skin	skin_eQTL
rs3886003	TRMT12	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125488200-125515800	Weak transcription	Lung	lung
2	chr8:125488200-125550400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:125489000-125519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr8:125489000-125531200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr8:125489000-125541200	Weak transcription	Gastric	stomach
6	chr8:125489000-125543400	Weak transcription	Small Intestine	intestine
7	chr8:125493200-125539400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr8:125496600-125549600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr8:125496800-125521200	Weak transcription	Fetal Heart	heart
10	chr8:125496800-125547400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr8:125499000-125537200	Weak transcription	Esophagus	oesophagus
12	chr8:125499200-125515800	Weak transcription	Right Ventricle	heart
13	chr8:125499800-125515800	Weak transcription	Colon Smooth Muscle	Colon
14	chr8:125500000-125526200	Weak transcription	Colonic Mucosa	Colon
15	chr8:125500000-125538000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr8:125500000-125538400	Weak transcription	Psoas Muscle	Psoas
17	chr8:125500000-125549600	Weak transcription	Fetal Brain Male	brain
18	chr8:125500200-125530800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr8:125500400-125526400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr8:125500600-125513800	Weak transcription	Fetal Kidney	kidney
21	chr8:125501600-125514800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr8:125501600-125514800	Weak transcription	GM12878-XiMat	blood
23	chr8:125501600-125516000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr8:125501600-125524600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr8:125501600-125535000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr8:125501600-125550000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr8:125501800-125514800	Weak transcription	HUVEC	blood vessel
28	chr8:125502000-125515800	Weak transcription	HSMMtube	muscle
29	chr8:125502400-125514800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr8:125502600-125514000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr8:125503800-125514800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr8:125503800-125514800	Weak transcription	Brain Anterior Caudate	brain
33	chr8:125503800-125515800	Weak transcription	Thymus	Thymus
34	chr8:125503800-125518800	Weak transcription	Brain Hippocampus Middle	brain
35	chr8:125504000-125513400	Weak transcription	Fetal Brain Female	brain
36	chr8:125504000-125514000	Weak transcription	Primary B cells from cord blood	blood
37	chr8:125504000-125515400	Weak transcription	Fetal Lung	lung
38	chr8:125504000-125515800	Weak transcription	HMEC	breast
39	chr8:125504000-125518800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr8:125504000-125518800	Weak transcription	Brain Substantia Nigra	brain
41	chr8:125504000-125521200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr8:125504000-125524800	Weak transcription	Pancreas	Pancrea
43	chr8:125504000-125525000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr8:125504000-125525800	Weak transcription	NHLF	lung
45	chr8:125504000-125550800	Weak transcription	Spleen	Spleen
46	chr8:125504200-125515000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr8:125504200-125515000	Weak transcription	Brain Germinal Matrix	brain
48	chr8:125504200-125515400	Weak transcription	NH-A	brain
49	chr8:125504400-125515000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr8:125504400-125518800	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links