Variant report

Variant	rs2729762
Chromosome Location	chr11:77033699-77033700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10899365	0.80[TSI][hapmap]
rs10899376	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs10899378	0.87[EUR][1000 genomes]
rs10899379	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11237173	0.91[EUR][1000 genomes]
rs11237189	0.86[EUR][1000 genomes]
rs11237193	0.87[EUR][1000 genomes]
rs11237195	0.90[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs11237196	0.86[EUR][1000 genomes]
rs11237199	0.83[CEU][hapmap]
rs12271542	0.86[EUR][1000 genomes]
rs12420360	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs1377470	0.95[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs1377471	0.92[EUR][1000 genomes]
rs1453343	0.86[EUR][1000 genomes]
rs1618188	0.80[TSI][hapmap]
rs1670459	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1793476	0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs1793483	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1793488	0.80[TSI][hapmap]
rs1840151	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2250639	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs2250647	0.95[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs2298793	0.95[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs2602458	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2602459	0.89[EUR][1000 genomes]
rs2602460	0.84[AFR][1000 genomes]
rs2602463	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2602464	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2602465	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2602468	0.92[EUR][1000 genomes]
rs2602469	0.92[EUR][1000 genomes]
rs2602470	0.92[EUR][1000 genomes]
rs2602472	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2602473	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs2602477	0.88[EUR][1000 genomes]
rs2602479	0.88[EUR][1000 genomes]
rs2602488	0.90[CEU][hapmap];0.96[EUR][1000 genomes]
rs2602489	0.97[EUR][1000 genomes]
rs2725810	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs2725812	0.91[JPT][hapmap]
rs2725815	0.97[EUR][1000 genomes]
rs2725816	0.90[EUR][1000 genomes]
rs2725826	0.98[EUR][1000 genomes]
rs2725827	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2725830	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2725831	0.93[EUR][1000 genomes]
rs2725832	0.91[EUR][1000 genomes]
rs2729747	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2729753	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729757	0.84[AFR][1000 genomes]
rs2729764	0.83[EUR][1000 genomes]
rs2729769	0.97[EUR][1000 genomes]
rs2729771	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2844328	0.88[EUR][1000 genomes]
rs2844332	0.88[EUR][1000 genomes]
rs2844333	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2844334	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs2844336	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2844337	0.95[CEU][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs2852381	0.81[AFR][1000 genomes]
rs2852383	0.84[AFR][1000 genomes]
rs2852384	0.88[EUR][1000 genomes]
rs2852385	0.91[EUR][1000 genomes]
rs2852388	0.86[YRI][hapmap]
rs2852390	0.88[LWK][hapmap];0.93[YRI][hapmap]
rs2852392	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs2852394	0.88[EUR][1000 genomes]
rs2853086	0.89[EUR][1000 genomes]
rs2853087	0.88[EUR][1000 genomes]
rs2853088	0.86[EUR][1000 genomes]
rs2853090	0.89[EUR][1000 genomes]
rs2853103	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs28858991	0.84[EUR][1000 genomes]
rs3015989	0.86[JPT][hapmap]
rs3015993	0.86[JPT][hapmap]
rs3018424	0.82[EUR][1000 genomes]
rs4590893	0.85[EUR][1000 genomes]
rs476925	0.95[JPT][hapmap]
rs482243	0.85[ASN][1000 genomes]
rs489038	0.82[ASN][1000 genomes]
rs4944158	0.81[ASN][1000 genomes]
rs4945162	0.91[JPT][hapmap]
rs4945166	0.91[JPT][hapmap]
rs4945169	0.81[ASN][1000 genomes]
rs495889	0.86[JPT][hapmap]
rs514191	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs575662	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs599437	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs674652	0.86[JPT][hapmap]
rs688212	0.95[JPT][hapmap]
rs7109645	0.85[TSI][hapmap]
rs7118869	0.95[JPT][hapmap]
rs7119033	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534515	chr11:76900813-77035769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats 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	29 gene(s)	inside rSNPs	diseases
5	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2729762	PAK1	cis	parietal	SCAN
rs2729762	RELT	cis	cerebellum	SCAN
rs2729762	UCP2	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77025000-77034200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:77025400-77037600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:77027400-77043000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:77027600-77043000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:77028000-77068400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:77028200-77066000	Weak transcription	Fetal Kidney	kidney
7	chr11:77028400-77043000	Weak transcription	Fetal Lung	lung
8	chr11:77030400-77043000	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:77030600-77086800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr11:77030800-77036800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:77030800-77046800	Weak transcription	Small Intestine	intestine
12	chr11:77030800-77054200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr11:77031200-77043000	Weak transcription	Colonic Mucosa	Colon
14	chr11:77031400-77036200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:77031400-77037200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:77031400-77037600	Strong transcription	Primary T cells from cord blood	blood
17	chr11:77031600-77034400	Strong transcription	Primary B cells from cord blood	blood
18	chr11:77031600-77037800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr11:77031600-77046600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr11:77031600-77066400	Weak transcription	Gastric	stomach
21	chr11:77031600-77073800	Weak transcription	Spleen	Spleen
22	chr11:77031800-77036000	Weak transcription	HMEC	breast
23	chr11:77031800-77070400	Weak transcription	Fetal Brain Male	brain
24	chr11:77032000-77033800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:77032000-77034400	Strong transcription	Fetal Intestine Large	intestine
26	chr11:77032000-77034400	Strong transcription	Fetal Muscle Leg	muscle
27	chr11:77032000-77034400	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr11:77032000-77034400	Strong transcription	GM12878-XiMat	blood
29	chr11:77032000-77035000	Strong transcription	Fetal Brain Female	brain
30	chr11:77032000-77035000	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr11:77032000-77037600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr11:77032000-77037800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr11:77032000-77037800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr11:77032000-77038000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:77032000-77038000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr11:77032000-77038000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr11:77032200-77037000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr11:77032200-77037800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:77032200-77066400	Weak transcription	Lung	lung
40	chr11:77032400-77034600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr11:77032400-77037800	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr11:77032400-77043000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:77032600-77037600	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr11:77032600-77037800	Strong transcription	Placenta	Placenta
45	chr11:77032600-77043200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr11:77032600-77046200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr11:77032800-77034400	Strong transcription	Aorta	Aorta
48	chr11:77032800-77035000	Strong transcription	Adipose Nuclei	Adipose
49	chr11:77032800-77037800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr11:77033000-77034400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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