Variant report

Variant	rs3105105
Chromosome Location	chr2:95848018-95848019
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:95841614..95845091-chr2:95847928..95851123,3	K562	blood:
2	chr2:95842139..95845316-chr2:95846030..95848957,3	MCF-7	breast:
3	chr2:95833553..95835805-chr2:95846574..95849112,2	K562	blood:
4	chr2:95847064..95848978-chr2:95850544..95852879,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10195614	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1104775	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11164122	0.81[CEU][hapmap]
rs11897976	0.95[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs12992066	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1559483	0.81[CEU][hapmap]
rs17119148	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1862897	0.95[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs1875402	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1966272	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2001254	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2010533	0.89[EUR][1000 genomes]
rs2042477	0.95[CEU][hapmap]
rs2098768	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2113417	0.95[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs2291991	0.83[EUR][1000 genomes]
rs2320339	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2320619	0.85[EUR][1000 genomes]
rs2320620	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2320621	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2320624	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3105098	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs3105099	0.89[ASW][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap]
rs3105100	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3105101	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3105102	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3105104	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112221	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112222	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3112223	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112225	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112228	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3112229	0.90[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3112230	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112231	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3112982	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs3112983	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs3112984	0.94[CEU][hapmap];0.84[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3112985	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3112986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3112987	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3112990	0.83[ASN][1000 genomes]
rs3112995	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112996	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112997	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112999	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3113000	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3113001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3113002	1.00[ASW][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap]
rs3755520	0.81[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs3755523	0.81[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs3755525	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs3772031	0.95[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs3772032	0.95[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs3772033	0.95[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs3772041	0.81[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs3772042	0.81[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs3772043	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs3772044	0.90[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs3821341	0.86[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs4241315	0.90[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs4854241	0.80[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap]
rs4854243	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4854244	0.84[EUR][1000 genomes]
rs4854247	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4854249	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6577012	0.81[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs6577013	0.81[CEU][hapmap];0.94[TSI][hapmap]
rs6715813	0.81[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs6719098	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6723333	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6725821	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6741001	0.95[CEU][hapmap]
rs6750542	0.95[CEU][hapmap]
rs7565772	0.90[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs7574862	0.81[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs7580685	0.81[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs7582368	0.90[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap]
rs7585473	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7585914	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7586229	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7594144	0.83[CEU][hapmap];0.83[JPT][hapmap]
rs870393	0.81[GIH][hapmap];0.94[TSI][hapmap]
rs872580	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs889851	0.81[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs889852	0.81[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs889853	0.81[CEU][hapmap]
rs918811	0.95[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs9678800	0.95[CEU][hapmap];0.91[TSI][hapmap]
rs9989786	0.81[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005016	chr2:95327875-95914467	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv482276	chr2:95711972-95888406	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv817299	chr2:95799814-96159275	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3105105	SRA1	trans	parietal	SCAN
rs3105105	KCNIP3	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95832800-95850200	Weak transcription	Hela-S3	cervix
2	chr2:95838400-95851400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:95839600-95849400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:95840400-95850200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:95841000-95849000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr2:95841000-95849200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:95841200-95850200	Strong transcription	HepG2	liver
8	chr2:95841800-95848800	Strong transcription	Rectal Mucosa Donor 31	rectum
9	chr2:95841800-95849200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:95841800-95849400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr2:95842000-95849000	Strong transcription	Brain Hippocampus Middle	brain
12	chr2:95842200-95849200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:95843000-95848200	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr2:95843000-95849000	Strong transcription	Brain Anterior Caudate	brain
15	chr2:95843000-95850200	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:95843200-95848200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
17	chr2:95843200-95849800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:95843200-95850000	ZNF genes & repeats	Liver	Liver
19	chr2:95843400-95848400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
20	chr2:95843600-95849200	Strong transcription	Fetal Brain Female	brain
21	chr2:95844000-95851000	Weak transcription	Stomach Mucosa	stomach
22	chr2:95845000-95849000	ZNF genes & repeats	A549	lung
23	chr2:95845000-95849200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr2:95845200-95848200	ZNF genes & repeats	Osteobl	bone
25	chr2:95845200-95848400	Strong transcription	Fetal Lung	lung
26	chr2:95845200-95848400	Strong transcription	Dnd41	blood
27	chr2:95845200-95848600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr2:95845200-95848600	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr2:95845200-95848600	Strong transcription	Colonic Mucosa	Colon
30	chr2:95845200-95848600	Strong transcription	HSMMtube	muscle
31	chr2:95845200-95849000	Strong transcription	Brain Substantia Nigra	brain
32	chr2:95845200-95849000	ZNF genes & repeats	Ovary	ovary
33	chr2:95845200-95849200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:95845200-95849200	Strong transcription	Brain Cingulate Gyrus	brain
35	chr2:95845200-95849200	Strong transcription	Placenta	Placenta
36	chr2:95845200-95849200	Strong transcription	Rectal Smooth Muscle	rectum
37	chr2:95845400-95848200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:95845400-95848200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:95845400-95848400	Strong transcription	Pancreas	Pancrea
40	chr2:95845400-95848600	Strong transcription	Brain Germinal Matrix	brain
41	chr2:95845400-95848600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:95845400-95849000	Strong transcription	Brain Angular Gyrus	brain
43	chr2:95845600-95848200	Strong transcription	Fetal Thymus	thymus
44	chr2:95845600-95848400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
45	chr2:95845600-95848600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:95845600-95849000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:95845800-95848200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:95845800-95848600	Strong transcription	Fetal Kidney	kidney
49	chr2:95845800-95849000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:95845800-95849000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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