Variant report

Variant	rs2602465
Chromosome Location	chr11:77107178-77107179
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr11:77107158-77107938	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
PAK1	TF binding region

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10899376	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs10899378	0.93[EUR][1000 genomes]
rs10899379	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11237173	0.97[EUR][1000 genomes]
rs11237189	0.93[EUR][1000 genomes]
rs11237193	0.93[EUR][1000 genomes]
rs11237195	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs11237196	0.92[EUR][1000 genomes]
rs11237199	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs12271542	0.92[EUR][1000 genomes]
rs1377470	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs1377471	0.96[EUR][1000 genomes]
rs1453343	0.90[EUR][1000 genomes]
rs1670459	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs1793476	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs1793483	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs1840151	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2250639	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs2250647	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs2298793	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs2602458	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2602459	0.95[EUR][1000 genomes]
rs2602463	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2602464	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs2602468	0.96[EUR][1000 genomes]
rs2602469	0.96[EUR][1000 genomes]
rs2602470	0.96[EUR][1000 genomes]
rs2602472	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602477	0.94[EUR][1000 genomes]
rs2602479	0.94[EUR][1000 genomes]
rs2602488	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs2602489	0.90[EUR][1000 genomes]
rs2725810	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs2725812	0.90[JPT][hapmap]
rs2725815	0.90[EUR][1000 genomes]
rs2725816	0.97[EUR][1000 genomes]
rs2725826	0.90[EUR][1000 genomes]
rs2725827	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs2725830	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2725831	0.97[EUR][1000 genomes]
rs2725832	0.95[EUR][1000 genomes]
rs2729747	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2729753	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2729762	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]
rs2729769	0.90[EUR][1000 genomes]
rs2729771	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2844328	0.94[EUR][1000 genomes]
rs2844332	0.94[EUR][1000 genomes]
rs2844333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844334	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs2844336	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2844337	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs2852384	0.94[EUR][1000 genomes]
rs2852385	0.95[EUR][1000 genomes]
rs2852392	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs2852394	0.94[EUR][1000 genomes]
rs2853086	0.95[EUR][1000 genomes]
rs2853087	0.94[EUR][1000 genomes]
rs2853088	0.93[EUR][1000 genomes]
rs2853090	0.95[EUR][1000 genomes]
rs2853103	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs3015989	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs3015993	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs4590893	0.90[EUR][1000 genomes]
rs473012	0.83[ASN][1000 genomes]
rs476925	0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4945162	0.90[JPT][hapmap]
rs4945166	0.90[JPT][hapmap]
rs495889	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs514191	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs517511	0.84[ASN][1000 genomes]
rs538670	0.81[ASN][1000 genomes]
rs539906	0.80[ASN][1000 genomes]
rs562939	0.80[ASN][1000 genomes]
rs568309	0.82[ASN][1000 genomes]
rs575662	0.95[JPT][hapmap]
rs584909	0.80[ASN][1000 genomes]
rs599437	0.95[JPT][hapmap]
rs605910	0.80[ASN][1000 genomes]
rs618012	0.80[ASN][1000 genomes]
rs635291	0.84[ASN][1000 genomes]
rs674652	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs688212	0.85[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7109645	0.83[EUR][1000 genomes]
rs7118869	0.95[JPT][hapmap]
rs7119033	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7943778	0.82[EUR][1000 genomes]
rs98703	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:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77046800-77121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:77055200-77117600	Weak transcription	Pancreas	Pancrea
3	chr11:77067200-77111800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:77084000-77111400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:77084600-77121200	Weak transcription	Thymus	Thymus
6	chr11:77086400-77108000	Weak transcription	Brain Anterior Caudate	brain
7	chr11:77086600-77120000	Weak transcription	Spleen	Spleen
8	chr11:77090800-77111200	Weak transcription	HMEC	breast
9	chr11:77091000-77108200	Weak transcription	Brain Angular Gyrus	brain
10	chr11:77091000-77112000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:77091000-77113400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:77091000-77117000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:77091000-77117600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:77093600-77117800	Weak transcription	NH-A	brain
15	chr11:77094000-77118400	Weak transcription	NHLF	lung
16	chr11:77094200-77111800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr11:77094200-77118200	Weak transcription	NHDF-Ad	bronchial
18	chr11:77094200-77118400	Weak transcription	Colonic Mucosa	Colon
19	chr11:77095400-77121000	Weak transcription	Fetal Thymus	thymus
20	chr11:77095800-77118600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr11:77097800-77111200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr11:77097800-77111200	Weak transcription	Fetal Muscle Leg	muscle
23	chr11:77098000-77121200	Weak transcription	Placenta	Placenta
24	chr11:77098200-77118400	Weak transcription	Fetal Stomach	stomach
25	chr11:77102600-77112400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr11:77102800-77111800	Weak transcription	Fetal Lung	lung
27	chr11:77102800-77116400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr11:77103000-77118400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr11:77103000-77121400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:77103200-77108600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr11:77103200-77112800	Weak transcription	Primary B cells from cord blood	blood
32	chr11:77103600-77109600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:77103800-77121000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr11:77103800-77122000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:77104000-77108000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr11:77104000-77112600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:77104200-77107600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr11:77104200-77108400	Weak transcription	Primary T cells from cord blood	blood
39	chr11:77104200-77108600	Weak transcription	Fetal Kidney	kidney
40	chr11:77104200-77111800	Weak transcription	HSMM	muscle
41	chr11:77104400-77107800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr11:77104600-77107800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr11:77104600-77111800	Weak transcription	Colon Smooth Muscle	Colon
44	chr11:77104600-77118400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr11:77106000-77108800	Enhancers	Duodenum Mucosa	Duodenum
46	chr11:77106000-77109000	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr11:77106000-77109000	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr11:77106000-77109000	Enhancers	Stomach Mucosa	stomach
49	chr11:77106000-77109800	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr11:77106200-77107400	Enhancers	A549	lung

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