Variant report

Variant	rs217198
Chromosome Location	chr10:116475099-116475100
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:116473831..116475798-chr10:116484185..116486243,2	MCF-7	breast:
2	chr10:116463984..116465623-chr10:116473581..116476078,2	MCF-7	breast:
3	chr10:116475010..116479006-chr10:116480936..116484073,4	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11196802	1.00[ASW][hapmap]
rs11196806	1.00[ASW][hapmap]
rs11196810	1.00[ASW][hapmap]
rs11196826	1.00[ASW][hapmap]
rs11196841	1.00[ASW][hapmap]
rs11196894	1.00[ASN][1000 genomes]
rs12768716	1.00[ASW][hapmap]
rs217185	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs217186	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs217188	1.00[GIH][hapmap];0.93[TSI][hapmap]
rs217197	0.83[EUR][1000 genomes]
rs2532819	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67402998	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808252	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808257	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808260	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808261	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808262	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808277	1.00[ASN][1000 genomes]
rs808278	1.00[ASN][1000 genomes]
rs808284	1.00[ASN][1000 genomes]
rs808292	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808293	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808297	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808300	1.00[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808304	1.00[ASN][1000 genomes]
rs808308	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808309	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808310	1.00[ASN][1000 genomes]
rs808311	1.00[ASN][1000 genomes]
rs808312	1.00[ASN][1000 genomes]
rs808315	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808317	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808318	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808319	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808320	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808324	1.00[ASN][1000 genomes]
rs808326	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808327	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808328	1.00[ASN][1000 genomes]
rs808329	1.00[ASN][1000 genomes]
rs808333	1.00[ASN][1000 genomes]
rs808334	1.00[ASN][1000 genomes]
rs808335	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808337	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808343	0.81[EUR][1000 genomes]
rs808345	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808354	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808356	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv1042170	chr10:116455043-116504871	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1046888	chr10:116455043-116505640	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv1038822	chr10:116455647-116497204	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs217198	LILRA3	trans	lymphoblastoid	seeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116471800-116475200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr10:116471800-116476800	Weak transcription	Right Ventricle	heart
3	chr10:116472600-116475400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr10:116472600-116475400	Enhancers	Aorta	Aorta
5	chr10:116472600-116476400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr10:116472600-116477400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr10:116472800-116475200	Weak transcription	Left Ventricle	heart
8	chr10:116472800-116475400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr10:116472800-116476800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr10:116473000-116475200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr10:116473000-116475200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr10:116473000-116475200	Enhancers	Fetal Lung	lung
13	chr10:116473000-116475400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr10:116473000-116475400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr10:116473000-116475400	Enhancers	NHDF-Ad	bronchial
16	chr10:116473000-116475600	Enhancers	Fetal Stomach	stomach
17	chr10:116473000-116475800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr10:116473000-116478200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr10:116473200-116475200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:116473200-116475600	Weak transcription	Brain Substantia Nigra	brain
21	chr10:116473400-116475200	Flanking Active TSS	NH-A	brain
22	chr10:116473400-116475400	Enhancers	HSMM	muscle
23	chr10:116473400-116476000	Enhancers	NHLF	lung
24	chr10:116473600-116475400	Flanking Active TSS	Osteobl	bone
25	chr10:116473600-116475800	Flanking Active TSS	Hela-S3	cervix
26	chr10:116473600-116478800	Weak transcription	Fetal Intestine Large	intestine
27	chr10:116473800-116476000	Enhancers	Right Atrium	heart
28	chr10:116473800-116476600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr10:116474000-116475200	Enhancers	HSMMtube	muscle
30	chr10:116474000-116475400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr10:116474000-116475400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr10:116474000-116475400	Enhancers	NHEK	skin
33	chr10:116474000-116475800	Enhancers	Stomach Mucosa	stomach
34	chr10:116474200-116475200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr10:116474200-116475400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr10:116474200-116475400	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr10:116474200-116475400	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr10:116474200-116475400	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr10:116474200-116475400	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr10:116474200-116475400	Enhancers	Stomach Smooth Muscle	stomach
41	chr10:116474200-116475600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr10:116474200-116482800	Weak transcription	Brain Angular Gyrus	brain
43	chr10:116474400-116475200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr10:116474400-116475200	Weak transcription	Gastric	stomach
45	chr10:116474400-116478200	Weak transcription	Fetal Muscle Leg	muscle
46	chr10:116474400-116479000	Weak transcription	Pancreas	Pancrea
47	chr10:116474400-116479000	Weak transcription	Small Intestine	intestine
48	chr10:116474400-116480600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr10:116474400-116480800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr10:116474400-116482200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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