Variant report

Variant	rs2602477
Chromosome Location	chr11:77147470-77147471
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10793246	0.80[CHD][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap]
rs10899365	0.80[CHD][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap]
rs10899369	0.84[CHD][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap]
rs10899376	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899378	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899379	0.91[CEU][hapmap];0.96[EUR][1000 genomes]
rs11237146	0.84[CHD][hapmap];0.87[MEX][hapmap]
rs11237147	0.84[CHD][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap]
rs11237173	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11237189	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237193	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237195	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11237196	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11237199	0.83[CHB][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12271542	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1377470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1377471	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1453343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1618188	0.84[CHD][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap]
rs1620915	0.80[CHD][hapmap];0.81[GIH][hapmap]
rs1670451	0.84[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap]
rs17135625	0.86[ASN][1000 genomes]
rs1793467	0.84[CHD][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap]
rs1793488	0.86[GIH][hapmap];0.87[MEX][hapmap]
rs1840151	0.98[EUR][1000 genomes]
rs1894214	0.84[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap]
rs2250639	0.95[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2250647	0.95[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2298793	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602458	0.98[EUR][1000 genomes]
rs2602459	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2602463	0.85[EUR][1000 genomes]
rs2602464	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2602465	0.90[CEU][hapmap];0.94[EUR][1000 genomes]
rs2602468	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602469	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602470	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602472	0.91[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs2602479	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2602488	0.90[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2602489	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2725810	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2725815	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2725816	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2725826	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2725827	0.95[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2725830	0.98[EUR][1000 genomes]
rs2725831	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2725832	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2729747	0.94[EUR][1000 genomes]
rs2729753	0.82[EUR][1000 genomes]
rs2729762	0.91[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs2729769	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2729771	0.85[EUR][1000 genomes]
rs2844328	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2844332	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844333	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2844334	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844336	0.87[EUR][1000 genomes]
rs2844337	0.95[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2852384	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852385	0.82[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2852392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852394	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2853086	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2853087	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2853088	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2853090	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2853103	0.89[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3018424	0.80[ASN][1000 genomes]
rs4590893	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7109645	0.86[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7119033	0.97[EUR][1000 genomes]
rs7943778	0.83[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9634031	0.87[JPT][hapmap]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2602477	PAK1	cis	cerebellum	SCAN
rs2602477	RELT	cis	cerebellum	SCAN
rs2602477	UCP2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77135400-77149000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:77141600-77148600	Weak transcription	Ovary	ovary
3	chr11:77142200-77164800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:77142400-77151600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr11:77142800-77156200	Weak transcription	Gastric	stomach
6	chr11:77145600-77148000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr11:77146800-77148000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:77146800-77148000	Flanking Active TSS	GM12878-XiMat	blood
9	chr11:77147000-77147600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
10	chr11:77147000-77147600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr11:77147000-77147800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:77147000-77148000	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr11:77147000-77148000	Enhancers	Fetal Lung	lung
14	chr11:77147000-77148200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr11:77147000-77148200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr11:77147000-77148200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:77147000-77148800	Enhancers	Fetal Intestine Large	intestine
18	chr11:77147000-77149000	Enhancers	Fetal Intestine Small	intestine
19	chr11:77147000-77149200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr11:77147000-77149200	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr11:77147000-77150400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr11:77147200-77147800	Weak transcription	Thymus	Thymus
23	chr11:77147200-77149000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr11:77147200-77149200	Enhancers	Pancreas	Pancrea
25	chr11:77147200-77149200	Enhancers	Small Intestine	intestine
26	chr11:77147200-77160200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr11:77147200-77160800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr11:77147400-77147600	Enhancers	Primary hematopoietic stem cells	blood
29	chr11:77147400-77147800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr11:77147400-77149000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr11:77147400-77149400	Enhancers	Stomach Mucosa	stomach

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