Variant report

Variant	rs2171513
Chromosome Location	chr3:112184927-112184928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATG3-3	chr3:112184773-112185230	NONHSAT091179

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs12632867	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[TSI][hapmap]
rs1386895	0.82[CEU][hapmap];0.81[CHB][hapmap];0.91[TSI][hapmap]
rs1398091	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs1533159	0.86[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs1844089	0.81[CHB][hapmap]
rs1873571	0.81[CHB][hapmap]
rs1873572	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2633556	0.83[ASN][1000 genomes]
rs2633557	0.83[ASN][1000 genomes]
rs2633560	0.84[ASN][1000 genomes]
rs2633562	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs2633563	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2633574	0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2633578	0.81[CHB][hapmap]
rs2633579	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2633580	0.81[CHB][hapmap]
rs2633582	0.81[CHB][hapmap]
rs2638016	0.81[CHB][hapmap]
rs2638017	0.81[CHB][hapmap]
rs2638019	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2638022	0.81[CHB][hapmap]
rs2638023	0.86[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap]
rs2638026	0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2638029	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2638031	0.81[CHB][hapmap]
rs2638032	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2638035	0.86[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap]
rs2638037	0.81[CHB][hapmap]
rs2638039	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs2705507	0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2705521	0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2705522	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2705534	0.81[CHB][hapmap]
rs2705535	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2705541	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2705544	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2705555	0.86[ASN][1000 genomes]
rs2705556	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2705559	0.81[CHB][hapmap]
rs2705562	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2705565	0.82[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap]
rs2705566	0.85[CHB][hapmap]
rs2933134	0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2933135	0.86[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs2952319	0.86[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs2952323	0.81[CHB][hapmap]
rs2952325	0.90[JPT][hapmap]
rs2952326	0.81[CHB][hapmap]
rs2952327	0.81[CHB][hapmap]
rs2969895	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2969896	0.86[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2971204	0.82[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2971205	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682410	0.91[TSI][hapmap]
rs6438079	0.82[CEU][hapmap];0.91[TSI][hapmap]
rs728568	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs9288952	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes]
rs9869579	1.00[CEU][hapmap];0.80[CHB][hapmap]
rs998036	0.88[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591294	chr3:112091220-112208750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1010208	chr3:112098542-112227212	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2171513	SLC35A5	cis	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112179800-112189800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:112180400-112195400	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr3:112181400-112185600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:112181600-112185000	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr3:112181800-112185600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr3:112182000-112185400	Enhancers	Primary hematopoietic stem cells	blood
7	chr3:112182200-112193600	Weak transcription	Spleen	Spleen
8	chr3:112182400-112185000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:112182800-112186400	Weak transcription	Fetal Thymus	thymus
10	chr3:112183400-112185200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr3:112183400-112185400	Genic enhancers	Primary B cells from cord blood	blood
12	chr3:112183600-112185000	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr3:112183600-112185200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr3:112183600-112185200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:112183600-112185400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:112183600-112185400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:112183600-112186400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:112183600-112186400	Weak transcription	Adipose Nuclei	Adipose
19	chr3:112183800-112185200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr3:112183800-112185200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:112183800-112186400	Weak transcription	Thymus	Thymus
22	chr3:112183800-112186800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr3:112183800-112188600	Weak transcription	HSMM	muscle
24	chr3:112183800-112195000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr3:112184000-112185000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:112184000-112185000	Weak transcription	Brain Substantia Nigra	brain
27	chr3:112184000-112186400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:112184000-112186600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
29	chr3:112184000-112186800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr3:112184200-112185000	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr3:112184200-112185000	Weak transcription	Small Intestine	intestine
32	chr3:112184200-112185200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:112184200-112188000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:112184200-112190600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
35	chr3:112184200-112191600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:112184400-112185600	Genic enhancers	GM12878-XiMat	blood
37	chr3:112184600-112185000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:112184600-112185400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr3:112184600-112185600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr3:112184600-112185600	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr3:112184600-112187200	Genic enhancers	Primary T cells from cord blood	blood
42	chr3:112184800-112185000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr3:112184800-112185200	Enhancers	H9 Cell Line	embryonic stem cell
44	chr3:112184800-112185200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:112184800-112185400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:112184800-112185800	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr3:112184800-112186400	Strong transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links