Variant report

Variant	rs3829252
Chromosome Location	chr11:9801451-9801452
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SWAP70-1	chr11:9800694-9801489	NONHSAT017945
2	lnc-SWAP70-1	chr11:9800906-9802122	NONHSAT017946

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1045634	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1056593	0.80[JPT][hapmap]
rs10770061	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840300	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10840301	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840302	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840304	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840307	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11042494	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042495	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042496	0.90[CEU][hapmap];0.95[EUR][1000 genomes]
rs11042497	0.81[EUR][1000 genomes]
rs11042498	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12786198	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1496475	0.85[JPT][hapmap]
rs1532422	0.85[JPT][hapmap]
rs16907071	0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2878800	0.85[JPT][hapmap]
rs360148	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360149	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3751001	0.95[ASN][1000 genomes]
rs3763862	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4910500	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910501	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910502	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910503	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910505	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs55934784	0.97[ASN][1000 genomes]
rs7102804	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7105203	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7113055	0.84[JPT][hapmap]
rs7113459	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7114514	0.84[JPT][hapmap]
rs7120754	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7124706	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7925875	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7936721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9795085	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9795121	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9795122	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9795123	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]

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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3829252	OR56A1	cis	cerebellum	SCAN
rs3829252	WEE1	cis	cerebellum	SCAN
rs3829252	OR2D2	cis	cerebellum	SCAN
rs3829252	ASCL3	cis	parietal	SCAN
rs3829252	CCKBR	cis	cerebellum	SCAN
rs3829252	OR56B4	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9780600-9813200	Weak transcription	Small Intestine	intestine
2	chr11:9781600-9809000	Weak transcription	Fetal Brain Male	brain
3	chr11:9781800-9801600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr11:9787800-9805200	Weak transcription	Colonic Mucosa	Colon
5	chr11:9788600-9801600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:9795200-9812800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr11:9796800-9803600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr11:9797200-9801800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:9797200-9802000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:9797400-9821800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr11:9797600-9801600	Weak transcription	Fetal Thymus	thymus
12	chr11:9797600-9803600	Strong transcription	Fetal Intestine Large	intestine
13	chr11:9797800-9811800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:9798000-9809000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr11:9798200-9805200	Weak transcription	Fetal Heart	heart
16	chr11:9798200-9810400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr11:9798400-9803600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:9798400-9805200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:9798600-9811600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:9798800-9803800	Strong transcription	Brain Germinal Matrix	brain
21	chr11:9798800-9805000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr11:9799000-9801600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr11:9799000-9803400	Strong transcription	NH-A	brain
24	chr11:9799000-9803600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:9799000-9803600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:9799000-9803800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr11:9799000-9803800	Strong transcription	Osteobl	bone
28	chr11:9799000-9804000	Strong transcription	NHLF	lung
29	chr11:9799000-9806200	Strong transcription	Fetal Muscle Leg	muscle
30	chr11:9799000-9809200	Strong transcription	Fetal Stomach	stomach
31	chr11:9799200-9801600	Strong transcription	Primary B cells from cord blood	blood
32	chr11:9799200-9803200	Strong transcription	Primary hematopoietic stem cells	blood
33	chr11:9799200-9803200	Strong transcription	NHEK	skin
34	chr11:9799200-9803600	Strong transcription	Fetal Kidney	kidney
35	chr11:9799200-9803800	Strong transcription	Fetal Lung	lung
36	chr11:9799200-9803800	Strong transcription	Stomach Smooth Muscle	stomach
37	chr11:9799200-9806200	Strong transcription	Adipose Nuclei	Adipose
38	chr11:9799200-9812000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:9799200-9812200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:9799400-9803600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr11:9799400-9803600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr11:9799400-9803600	Strong transcription	NHDF-Ad	bronchial
43	chr11:9799600-9805400	Weak transcription	Right Atrium	heart
44	chr11:9799600-9806200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr11:9799600-9810600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr11:9799600-9823400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr11:9799800-9801600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr11:9799800-9803600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:9799800-9811600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr11:9799800-9812000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links