Variant report

Variant	rs2250639
Chromosome Location	chr11:77069790-77069791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10793246	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs10899364	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs10899365	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs10899369	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs10899376	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899378	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899379	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs11237145	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs11237146	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs11237147	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs11237173	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11237189	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11237193	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11237195	0.95[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11237196	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11237199	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs12271542	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12274255	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs12287216	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs12287680	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs1377470	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1377471	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1453343	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1613357	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs1618188	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1620915	0.84[JPT][hapmap]
rs1670451	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1670452	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs1670453	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs1670454	0.80[ASN][1000 genomes]
rs17135625	0.94[ASN][1000 genomes]
rs1793469	0.80[ASN][1000 genomes]
rs1793470	0.80[ASN][1000 genomes]
rs1793488	0.83[JPT][hapmap]
rs1840151	0.94[EUR][1000 genomes]
rs1894214	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1946005	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs2250647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298793	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2602458	0.94[EUR][1000 genomes]
rs2602459	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2602463	0.87[EUR][1000 genomes]
rs2602464	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602465	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs2602468	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2602469	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2602470	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2602472	0.95[CEU][hapmap];0.98[EUR][1000 genomes]
rs2602477	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2602479	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2602488	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2602489	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2725810	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2725815	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2725816	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2725826	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2725827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2725830	0.94[EUR][1000 genomes]
rs2725831	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2725832	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2729747	0.95[EUR][1000 genomes]
rs2729753	0.85[EUR][1000 genomes]
rs2729762	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs2729764	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2729769	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2729771	0.87[EUR][1000 genomes]
rs2844328	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2844332	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2844333	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs2844334	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2844336	0.88[EUR][1000 genomes]
rs2844337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2852384	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2852385	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852392	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2852394	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2853086	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2853087	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2853088	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2853090	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2853096	0.84[CHB][hapmap]
rs2853103	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3018424	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4590893	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7104166	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs7104295	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs7109645	0.82[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs7119033	0.93[EUR][1000 genomes]
rs7121483	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs7938075	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs7943778	0.84[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs9634031	0.82[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77030600-77086800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr11:77031600-77073800	Weak transcription	Spleen	Spleen
3	chr11:77031800-77070400	Weak transcription	Fetal Brain Male	brain
4	chr11:77033400-77090400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr11:77034400-77086200	Weak transcription	NHLF	lung
6	chr11:77042800-77080800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr11:77043400-77072600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:77043400-77074800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:77043400-77082400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr11:77043400-77083600	Weak transcription	Thymus	Thymus
11	chr11:77043800-77071400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:77043800-77088400	Weak transcription	Colonic Mucosa	Colon
13	chr11:77044200-77075000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr11:77044600-77071600	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:77046200-77077000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:77046200-77092400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr11:77046800-77121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr11:77047200-77096000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:77047400-77089000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr11:77047400-77090000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr11:77047800-77075000	Weak transcription	Left Ventricle	heart
22	chr11:77047800-77075600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr11:77048600-77070000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr11:77048600-77087800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr11:77050400-77072000	Strong transcription	Primary T cells from cord blood	blood
26	chr11:77052600-77085600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr11:77055000-77085000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr11:77055200-77083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr11:77055200-77092200	Weak transcription	Small Intestine	intestine
30	chr11:77055200-77117600	Weak transcription	Pancreas	Pancrea
31	chr11:77057400-77088000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr11:77058600-77075000	Weak transcription	NH-A	brain
33	chr11:77059800-77085800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:77059800-77088800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr11:77060400-77084000	Weak transcription	Fetal Stomach	stomach
36	chr11:77063000-77070400	Strong transcription	Primary B cells from cord blood	blood
37	chr11:77063000-77072000	Weak transcription	NHDF-Ad	bronchial
38	chr11:77063200-77081000	Weak transcription	Stomach Mucosa	stomach
39	chr11:77063400-77070200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr11:77063400-77070400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:77063400-77070400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr11:77063400-77070800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr11:77063400-77071000	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:77063400-77071600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:77063800-77070400	Strong transcription	Fetal Intestine Large	intestine
46	chr11:77064000-77070800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr11:77064200-77102800	Weak transcription	Brain Substantia Nigra	brain
48	chr11:77064400-77070800	Weak transcription	NHEK	skin
49	chr11:77064600-77070000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr11:77064600-77072000	Weak transcription	Muscle Satellite Cultured Cells	--

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