Variant report

Variant	rs10838543
Chromosome Location	chr11:5717762-5717763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	11:5033143-5038367..11:5714465-5718134	Hela-S3	cervix:
2	11:5349791-5355747..11:5714465-5718134	GM12878	blood:
3	11:4988858-5002113..11:5714465-5718134	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HBG2-1	chr11:5717300-5718052	NONHSAT017688

Variant related genes	Relation type
ENSG00000224300	Chromatin interaction
ENSG00000225003	Chromatin interaction
ENSG00000236359	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10838544	0.99[ASN][1000 genomes]
rs10838545	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10838546	0.83[ASN][1000 genomes]
rs11038746	0.98[ASN][1000 genomes]
rs12274260	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12289981	0.82[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12294511	0.82[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12421805	0.93[ASN][1000 genomes]
rs12786295	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4910574	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910836	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910837	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55636303	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55986098	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7935564	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.98[ASN][1000 genomes]
rs7935903	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7935929	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7936676	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv896939	chr11:5497799-5809548	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv1041568	chr11:5585716-5765688	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1053414	chr11:5612989-6030212	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv553273	chr11:5639873-5871831	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
9	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
10	nsv896948	chr11:5701281-5719667	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv896949	chr11:5711177-5722444	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10838543	OR52M1	cis	cerebellum	SCAN
rs10838543	OR56B1	cis	cerebellum	SCAN
rs10838543	OR51B4	cis	cerebellum	SCAN
rs10838543	RBM45	trans	lymphoblastoid	RTeQTL
rs10838543	DNHD1	cis	cerebellum	SCAN
rs10838543	OR52W1	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5711600-5717800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr11:5712000-5723000	Weak transcription	Fetal Stomach	stomach
3	chr11:5712200-5717800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:5712200-5719400	Weak transcription	Gastric	stomach
5	chr11:5712200-5723600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:5712200-5725200	Weak transcription	Fetal Heart	heart
7	chr11:5712400-5719400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:5712400-5723000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:5712400-5723000	Weak transcription	Fetal Intestine Large	intestine
10	chr11:5712400-5730200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr11:5712400-5730600	Weak transcription	Fetal Lung	lung
12	chr11:5712400-5731800	Weak transcription	NH-A	brain
13	chr11:5712400-5732400	Weak transcription	Pancreas	Pancrea
14	chr11:5712400-5732400	Weak transcription	Stomach Mucosa	stomach
15	chr11:5712600-5717800	Weak transcription	Placenta	Placenta
16	chr11:5712600-5723800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr11:5712600-5729200	Weak transcription	Esophagus	oesophagus
18	chr11:5712600-5730200	Weak transcription	NHEK	skin
19	chr11:5712600-5732000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:5712600-5732600	Weak transcription	Colonic Mucosa	Colon
21	chr11:5713000-5723000	Weak transcription	Right Ventricle	heart
22	chr11:5713000-5726000	Weak transcription	Left Ventricle	heart
23	chr11:5713000-5734600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr11:5713600-5730800	Weak transcription	Brain Anterior Caudate	brain
25	chr11:5713600-5734800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:5713600-5745800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr11:5713800-5729800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr11:5713800-5731200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr11:5714000-5718000	Genic enhancers	Primary B cells from peripheral blood	blood
30	chr11:5714000-5718400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
31	chr11:5714000-5719400	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:5714000-5719400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr11:5714000-5732600	Weak transcription	Brain Substantia Nigra	brain
34	chr11:5714200-5717800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr11:5715000-5721400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr11:5715200-5733000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr11:5715800-5718000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr11:5715800-5729200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:5716000-5717800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr11:5716200-5719400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr11:5716200-5719400	Weak transcription	Small Intestine	intestine
42	chr11:5716200-5720400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:5716200-5721000	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr11:5716200-5721400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr11:5716200-5724200	Strong transcription	Osteobl	bone
46	chr11:5716600-5719200	Strong transcription	GM12878-XiMat	blood
47	chr11:5716800-5721200	Strong transcription	Primary B cells from cord blood	blood
48	chr11:5717000-5718000	Genic enhancers	HSMM	muscle
49	chr11:5717000-5720000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr11:5717000-5720000	Strong transcription	Aorta	Aorta

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