Variant report

Variant	rs12271542
Chromosome Location	chr11:77175552-77175553
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10899376	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899378	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899379	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs11237173	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11237189	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237193	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237195	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11237196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11237199	0.80[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1377470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1377471	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1453343	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1613357	0.83[CHB][hapmap];1.00[YRI][hapmap]
rs1618188	0.82[CHB][hapmap]
rs1620915	1.00[YRI][hapmap]
rs1670451	0.82[CHB][hapmap]
rs1670452	0.83[CHB][hapmap];1.00[YRI][hapmap]
rs1670453	0.83[CHB][hapmap];1.00[YRI][hapmap]
rs1670460	1.00[YRI][hapmap]
rs17135625	0.86[ASN][1000 genomes]
rs1793466	1.00[YRI][hapmap]
rs1793488	1.00[YRI][hapmap]
rs1840151	0.95[EUR][1000 genomes]
rs1946005	0.83[CHB][hapmap];1.00[YRI][hapmap]
rs2250639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2250647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2298793	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602458	0.95[EUR][1000 genomes]
rs2602459	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2602463	0.83[EUR][1000 genomes]
rs2602464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2602465	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs2602468	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602469	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602470	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602472	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs2602477	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602479	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602488	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2602489	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2725810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2725815	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2725816	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2725826	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2725827	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2725830	0.95[EUR][1000 genomes]
rs2725831	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2725832	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2729747	0.91[EUR][1000 genomes]
rs2729762	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs2729769	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2729771	0.83[EUR][1000 genomes]
rs2844328	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2844332	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844333	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs2844334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844336	0.85[EUR][1000 genomes]
rs2844337	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2852384	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852385	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2852392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852394	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2853086	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2853087	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2853088	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2853090	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2853103	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3018424	0.80[ASN][1000 genomes]
rs4590893	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56015509	1.00[AFR][1000 genomes]
rs7109645	0.82[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7119033	0.94[EUR][1000 genomes]
rs7943778	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	esv3437433	chr11:77101280-77291686	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77155400-77181400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:77160600-77178000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:77161200-77179200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:77167800-77182000	Weak transcription	Fetal Kidney	kidney
5	chr11:77168600-77178800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr11:77168800-77179600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr11:77169000-77181400	Weak transcription	Brain Angular Gyrus	brain
8	chr11:77170400-77176200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr11:77170400-77178000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr11:77170600-77178000	Weak transcription	Small Intestine	intestine
11	chr11:77170800-77178200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr11:77170800-77179000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:77171200-77181600	Weak transcription	Primary B cells from cord blood	blood
14	chr11:77172200-77178000	Weak transcription	Stomach Mucosa	stomach
15	chr11:77172200-77178200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:77172800-77176000	Weak transcription	Psoas Muscle	Psoas
17	chr11:77173400-77176400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr11:77173800-77183800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:77174200-77176000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr11:77174200-77176000	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr11:77174200-77176200	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr11:77174600-77180400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr11:77174800-77176000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr11:77174800-77179000	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr11:77175000-77175600	Enhancers	GM12878-XiMat	blood
26	chr11:77175000-77179000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr11:77175200-77175600	Enhancers	Fetal Intestine Small	intestine
28	chr11:77175200-77175800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr11:77175400-77175800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr11:77175400-77175800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:77175400-77176000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr11:77175400-77178200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:77175400-77179200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:77175400-77181400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links