Variant report

Variant	rs11196999
Chromosome Location	chr10:116700632-116700633
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:116260065..116262593-chr10:116698525..116701420,2	MCF-7	breast:
2	chr10:116666525..116669510-chr10:116698929..116700670,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229668	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10160015	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10444099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045657	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10490908	1.00[JPT][hapmap]
rs10510008	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10885631	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10885632	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10885633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885634	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10885636	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10885637	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885638	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885639	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196983	0.86[ASN][1000 genomes]
rs11196984	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs11196989	0.86[ASN][1000 genomes]
rs11196991	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197000	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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197005	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197006	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11197007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197010	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11197011	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197023	0.95[ASN][1000 genomes]
rs12098332	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12246008	0.95[ASN][1000 genomes]
rs12265048	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12269261	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12761122	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12764662	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12772737	0.95[ASN][1000 genomes]
rs12774597	0.95[ASN][1000 genomes]
rs12775180	1.00[JPT][hapmap]
rs12779231	0.95[ASN][1000 genomes]
rs17092542	1.00[JPT][hapmap]
rs17721283	1.00[JPT][hapmap]
rs17721905	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17722042	0.95[ASN][1000 genomes]
rs17794346	1.00[JPT][hapmap]
rs17795104	0.95[ASN][1000 genomes]
rs17795212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1966384	1.00[JPT][hapmap]
rs2095379	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105001	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2420070	0.86[ASN][1000 genomes]
rs34170154	0.95[ASN][1000 genomes]
rs34434610	0.95[ASN][1000 genomes]
rs34453431	0.95[ASN][1000 genomes]
rs34461950	0.87[ASN][1000 genomes]
rs35501899	0.95[ASN][1000 genomes]
rs35811923	0.95[ASN][1000 genomes]
rs3931556	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869271	0.95[ASN][1000 genomes]
rs61869272	0.95[ASN][1000 genomes]
rs61869274	0.95[ASN][1000 genomes]
rs61869275	0.95[ASN][1000 genomes]
rs6585302	0.86[ASN][1000 genomes]
rs6585306	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6585309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6585310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6585311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6585313	0.95[ASN][1000 genomes]
rs7071789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7071812	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072356	1.00[JPT][hapmap]
rs7074729	1.00[JPT][hapmap]
rs7075888	1.00[JPT][hapmap]
rs7079234	0.95[ASN][1000 genomes]
rs7085964	0.95[ASN][1000 genomes]
rs7093282	0.83[ASN][1000 genomes]
rs7093330	0.95[ASN][1000 genomes]
rs7094072	1.00[JPT][hapmap]
rs7097580	0.95[ASN][1000 genomes]
rs7099565	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7099590	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7099779	1.00[ASN][1000 genomes]
rs7100026	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7100159	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100894	0.86[ASN][1000 genomes]
rs72836518	0.95[ASN][1000 genomes]
rs749649	1.00[JPT][hapmap]
rs7895551	1.00[JPT][hapmap]
rs7898249	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7904605	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7908069	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908464	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909566	1.00[JPT][hapmap]
rs7909657	1.00[JPT][hapmap]
rs7917523	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7923295	1.00[JPT][hapmap]
rs881192	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs968848	0.95[ASN][1000 genomes]
rs968849	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv831996	chr10:116601552-116772968	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1039002	chr10:116643095-116879483	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv2761634	chr10:116643095-116879495	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription 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	10 gene(s)	inside rSNPs	diseases
8	nsv1045654	chr10:116654574-116879483	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats 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	10 gene(s)	inside rSNPs	diseases
9	nsv1043242	chr10:116655057-116883386	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv831997	chr10:116689552-116855698	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11196999	TECTB	cis	cerebellum	SCAN
rs11196999	ADRB1	cis	parietal	SCAN
rs11196999	TRUB1	cis	parietal	SCAN
rs11196999	TRUB1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116698600-116702400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr10:116698800-116702400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:116698800-116702600	Weak transcription	Lung	lung
4	chr10:116698800-116702800	Weak transcription	Gastric	stomach
5	chr10:116698800-116702800	Weak transcription	Pancreas	Pancrea
6	chr10:116698800-116703200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:116698800-116730400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr10:116698800-116763600	Weak transcription	Esophagus	oesophagus
9	chr10:116699000-116701000	Enhancers	Colon Smooth Muscle	Colon
10	chr10:116699000-116705000	Weak transcription	Colonic Mucosa	Colon
11	chr10:116699000-116706400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr10:116699200-116700800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr10:116699200-116700800	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr10:116699200-116700800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr10:116699200-116701000	Weak transcription	Fetal Muscle Leg	muscle
16	chr10:116699200-116701000	Enhancers	NHDF-Ad	bronchial
17	chr10:116699200-116702200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr10:116699200-116702400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr10:116699200-116702400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr10:116699200-116702400	Weak transcription	Left Ventricle	heart
21	chr10:116699200-116702400	Weak transcription	Right Ventricle	heart
22	chr10:116699200-116702400	Weak transcription	Small Intestine	intestine
23	chr10:116699200-116702400	Weak transcription	Thymus	Thymus
24	chr10:116699200-116702400	Weak transcription	Spleen	Spleen
25	chr10:116699200-116704800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr10:116699200-116705200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr10:116699200-116722400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr10:116699200-116722600	Weak transcription	Aorta	Aorta
29	chr10:116699400-116700800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr10:116699400-116700800	Enhancers	Fetal Heart	heart
31	chr10:116699400-116700800	Enhancers	A549	lung
32	chr10:116699400-116701000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr10:116699400-116701000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr10:116699400-116701000	Weak transcription	Fetal Stomach	stomach
35	chr10:116699400-116701200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr10:116699400-116702000	Weak transcription	Liver	Liver
37	chr10:116699400-116702200	Weak transcription	Brain Substantia Nigra	brain
38	chr10:116699400-116702200	Weak transcription	HSMM	muscle
39	chr10:116699400-116702400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr10:116699400-116702400	Weak transcription	HSMMtube	muscle
41	chr10:116699400-116702600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr10:116699400-116704200	Weak transcription	Stomach Mucosa	stomach
43	chr10:116699400-116708000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr10:116699600-116700800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr10:116699600-116700800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr10:116699600-116700800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr10:116699600-116701000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr10:116699600-116701000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr10:116699600-116701000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr10:116699600-116701000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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