Variant report

Variant	rs3751068
Chromosome Location	chr11:8946950-8946951
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:8941546..8948177-chr11:8950032..8955141,6	MCF-7	breast:
2	chr11:8940620..8943003-chr11:8946457..8949397,2	MCF-7	breast:
3	chr11:8718539..8720292-chr11:8944673..8947181,2	K562	blood:

Variant related genes	Relation type
ENSG00000176029	Chromatin interaction
ENSG00000166444	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10219366	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10734639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10743094	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769976	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10769977	1.00[CEU][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10840150	0.83[AMR][1000 genomes]
rs10840151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840153	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840154	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840155	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10840156	0.91[CEU][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11042128	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11042129	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11042131	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1133833	0.81[MEX][hapmap]
rs1136966	0.86[MEX][hapmap]
rs12794962	0.80[GIH][hapmap];0.81[MEX][hapmap]
rs12798311	0.83[EUR][1000 genomes]
rs1347016	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2016844	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2043218	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056903	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs2116510	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2116511	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2163625	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2246878	0.83[EUR][1000 genomes]
rs2247038	0.83[EUR][1000 genomes]
rs2316523	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2316541	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2568029	0.81[MEX][hapmap]
rs2568034	0.91[CEU][hapmap]
rs2568042	0.91[CEU][hapmap];0.91[TSI][hapmap]
rs2568047	0.82[GIH][hapmap];0.81[MEX][hapmap]
rs2568069	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2568074	0.83[EUR][1000 genomes]
rs2568075	0.83[EUR][1000 genomes]
rs2568077	0.83[EUR][1000 genomes]
rs2568079	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2568081	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2568086	0.87[AMR][1000 genomes]
rs2568087	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2568088	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2653556	0.87[CEU][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs2653565	0.91[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2653590	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2653594	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2653597	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2653601	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs2653604	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2653611	0.81[EUR][1000 genomes]
rs2742486	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2742487	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2742488	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2742489	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2742491	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2742493	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2742494	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2742495	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs2742496	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2742497	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2742502	0.86[MEX][hapmap]
rs2742504	0.81[EUR][1000 genomes]
rs2742505	0.81[EUR][1000 genomes]
rs2742512	0.83[EUR][1000 genomes]
rs2742513	0.83[EUR][1000 genomes]
rs2742514	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2742519	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2742521	0.91[CEU][hapmap]
rs3751063	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3751065	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763911	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3763912	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4370967	0.80[GIH][hapmap]
rs4909951	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910181	0.95[ASN][1000 genomes]
rs6486061	0.87[CHD][hapmap];0.84[JPT][hapmap]
rs7106152	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7125458	0.81[MEX][hapmap]
rs7932377	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7936201	0.81[MEX][hapmap]
rs7942026	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7951226	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs909464	0.83[EUR][1000 genomes]
rs9300096	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs982273	0.87[CEU][hapmap]

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	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS 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	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv435923	chr11:8839325-9000602	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv832062	chr11:8849295-9009472	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer 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	31 gene(s)	inside rSNPs	diseases
5	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3751068	TMEM9B	cis	parietal	SCAN
rs3751068	C11orf17	cis	lymphoblastoid	seeQTL
rs3751068	C11orf17	cis	Lymphoblastoid	GTEx
rs3751068	C11orf17	cis	multi-tissue	Pritchard
rs3751068	MRVI1	cis	cerebellum	SCAN
rs3751068	C11orf17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8933400-8947800	Weak transcription	Small Intestine	intestine
2	chr11:8934000-8952200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:8934200-8948800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:8936400-8951200	Weak transcription	Right Atrium	heart
5	chr11:8936600-8948600	Strong transcription	Fetal Thymus	thymus
6	chr11:8936600-8949000	Strong transcription	Fetal Stomach	stomach
7	chr11:8936600-8954000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr11:8936800-8947000	Strong transcription	Dnd41	blood
9	chr11:8936800-8947600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr11:8937000-8947600	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr11:8937000-8948200	Strong transcription	Fetal Brain Female	brain
12	chr11:8937200-8947400	Strong transcription	Thymus	Thymus
13	chr11:8937800-8947400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:8938000-8947400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr11:8938000-8947600	Strong transcription	Brain Cingulate Gyrus	brain
16	chr11:8938200-8947000	Strong transcription	Brain Anterior Caudate	brain
17	chr11:8938200-8947200	Strong transcription	Brain Germinal Matrix	brain
18	chr11:8939000-8947400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:8939000-8947600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr11:8939000-8948200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr11:8939400-8948200	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr11:8939400-8948800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr11:8939600-8947000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr11:8939800-8947600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:8939800-8947600	Strong transcription	Lung	lung
26	chr11:8940000-8948400	Strong transcription	Spleen	Spleen
27	chr11:8940200-8948600	Strong transcription	Stomach Smooth Muscle	stomach
28	chr11:8940200-8949200	Weak transcription	Primary B cells from cord blood	blood
29	chr11:8940400-8947200	Strong transcription	Fetal Muscle Leg	muscle
30	chr11:8940800-8947400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr11:8940800-8949200	Weak transcription	Fetal Heart	heart
32	chr11:8941200-8953400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr11:8941200-8956200	Weak transcription	K562	blood
34	chr11:8942000-8948800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr11:8942400-8950200	Weak transcription	Esophagus	oesophagus
36	chr11:8942400-8959000	Weak transcription	Fetal Kidney	kidney
37	chr11:8942600-8948800	Weak transcription	Colonic Mucosa	Colon
38	chr11:8943200-8950000	Weak transcription	GM12878-XiMat	blood
39	chr11:8943200-8950800	Weak transcription	Primary T cells from cord blood	blood
40	chr11:8943800-8969200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr11:8944000-8952200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr11:8944200-8956400	Weak transcription	HUVEC	blood vessel
43	chr11:8944600-8950000	Weak transcription	HMEC	breast
44	chr11:8944600-8950000	Weak transcription	HSMMtube	muscle
45	chr11:8944600-8950800	Weak transcription	HepG2	liver
46	chr11:8944600-8985000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:8944800-8949000	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr11:8944800-8949200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr11:8944800-8949600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr11:8944800-8950200	Weak transcription	Placenta	Placenta

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