Variant report

Variant	rs2298793
Chromosome Location	chr11:77090518-77090519
allele	C/T
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	STAT3	chr11:77090396-77090657	MCF10A-Er-Src	breast:	n/a	n/a
2	YY1	chr11:77090430-77090786	SK-N-SH	brain:	n/a	n/a
3	FOSL2	chr11:77090360-77090873	SK-N-SH	brain:	n/a	chr11:77090597-77090609
4	PBX3	chr11:77090367-77090797	SK-N-SH	brain:	n/a	n/a
5	PBX3	chr11:77090237-77090745	SK-N-SH	brain:	n/a	n/a
6	GATA2	chr11:77090398-77090743	HUVEC	blood vessel:	n/a	n/a
7	TCF12	chr11:77090208-77090797	SK-N-SH	brain:	n/a	n/a
8	FOS	chr11:77090388-77090688	MCF10A-Er-Src	breast:	n/a	chr11:77090597-77090609 chr11:77090536-77090547
9	STAT3	chr11:77090388-77090537	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr11:77090393-77090688	MCF10A-Er-Src	breast:	n/a	chr11:77090597-77090609 chr11:77090536-77090547
11	TCF12	chr11:77090187-77090872	SK-N-SH	brain:	n/a	n/a
12	FOS	chr11:77090438-77090670	MCF10A-Er-Src	breast:	n/a	chr11:77090597-77090609 chr11:77090536-77090547
13	FOS	chr11:77090360-77090761	HUVEC	blood vessel:	n/a	chr11:77090597-77090609 chr11:77090536-77090547

Variant related genes	Relation type
PAK1	TF binding region

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10793246	1.00[ASW][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs10899363	1.00[YRI][hapmap]
rs10899364	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs10899365	1.00[ASW][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs10899369	1.00[ASW][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs10899376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899378	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899379	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs11237145	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs11237146	1.00[ASW][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs11237147	0.96[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];1.00[YRI][hapmap]
rs11237173	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237189	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11237193	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11237195	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11237196	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11237199	0.83[CHB][hapmap];0.86[EUR][1000 genomes]
rs12271542	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12274255	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs12287216	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs12287680	0.83[JPT][hapmap]
rs1377470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1377471	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1453343	1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1540217	0.80[AMR][1000 genomes]
rs1613357	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs1618188	1.00[ASW][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap]
rs1620915	1.00[ASW][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs1628438	0.80[AMR][1000 genomes]
rs1670451	0.96[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs1670452	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs1670453	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs1670454	0.80[AMR][1000 genomes]
rs1670457	0.80[AMR][1000 genomes]
rs1670460	1.00[YRI][hapmap]
rs17135625	0.95[ASN][1000 genomes]
rs1793466	1.00[YRI][hapmap]
rs1793467	1.00[ASW][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap]
rs1793469	0.80[AMR][1000 genomes]
rs1793470	0.80[AMR][1000 genomes]
rs1793488	1.00[ASW][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs1840151	0.94[EUR][1000 genomes]
rs1894214	0.96[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs1946005	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs2250639	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]
rs2250647	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2602458	0.94[EUR][1000 genomes]
rs2602459	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2602463	0.87[EUR][1000 genomes]
rs2602464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2602465	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs2602468	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602469	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602470	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2602472	0.95[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs2602477	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602479	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602488	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2602489	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2725810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2725815	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2725816	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2725826	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2725827	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2725830	0.94[EUR][1000 genomes]
rs2725831	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2725832	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2729747	0.97[EUR][1000 genomes]
rs2729753	0.82[EUR][1000 genomes]
rs2729762	0.95[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs2729764	0.86[ASN][1000 genomes]
rs2729769	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2729771	0.87[EUR][1000 genomes]
rs2844328	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2844332	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2844333	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs2844334	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2844336	0.88[EUR][1000 genomes]
rs2844337	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2852384	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2852385	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2852392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2852394	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2853086	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2853087	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2853088	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2853090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2853096	1.00[YRI][hapmap]
rs2853103	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3018424	0.89[ASN][1000 genomes]
rs4590893	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56015509	0.84[AFR][1000 genomes]
rs7104166	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs7104295	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs7109645	0.82[CEU][hapmap];0.84[CHB][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs7119033	0.93[EUR][1000 genomes]
rs7121483	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs7938075	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs7943778	0.83[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs9634031	0.93[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2298793	PAK1	cis	cerebellum	SCAN
rs2298793	UCP2	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77046200-77092400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr11:77046800-77121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:77047200-77096000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:77055200-77092200	Weak transcription	Small Intestine	intestine
5	chr11:77055200-77117600	Weak transcription	Pancreas	Pancrea
6	chr11:77064200-77102800	Weak transcription	Brain Substantia Nigra	brain
7	chr11:77067000-77092800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr11:77067000-77093800	Weak transcription	Psoas Muscle	Psoas
9	chr11:77067000-77097000	Weak transcription	Esophagus	oesophagus
10	chr11:77067200-77111800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr11:77068800-77097000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr11:77070000-77102000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr11:77075200-77097200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr11:77077200-77091800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr11:77077600-77092800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:77078000-77091600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr11:77081000-77093400	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr11:77081000-77094600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:77081200-77091000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:77081200-77091600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:77081200-77091800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:77081200-77095600	Strong transcription	GM12878-XiMat	blood
23	chr11:77081200-77096600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr11:77082000-77095600	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr11:77082000-77096200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:77082200-77091200	Strong transcription	Placenta	Placenta
27	chr11:77082200-77091400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr11:77082200-77091400	Strong transcription	Primary T cells from cord blood	blood
29	chr11:77082200-77092800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:77082200-77095800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr11:77082400-77090600	Weak transcription	Right Ventricle	heart
32	chr11:77082400-77104200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr11:77083000-77091000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr11:77083200-77092000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:77083400-77091000	Strong transcription	Fetal Muscle Leg	muscle
36	chr11:77083400-77091600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr11:77084000-77093200	Weak transcription	Hela-S3	cervix
38	chr11:77084000-77111400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:77084200-77107000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr11:77084400-77091200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr11:77084400-77103600	Weak transcription	Fetal Kidney	kidney
42	chr11:77084600-77121200	Weak transcription	Thymus	Thymus
43	chr11:77085600-77092800	Weak transcription	HSMMtube	muscle
44	chr11:77086400-77093400	Weak transcription	Stomach Mucosa	stomach
45	chr11:77086400-77108000	Weak transcription	Brain Anterior Caudate	brain
46	chr11:77086600-77090800	Weak transcription	A549	lung
47	chr11:77086600-77092800	Weak transcription	NHLF	lung
48	chr11:77086600-77102200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:77086600-77120000	Weak transcription	Spleen	Spleen
50	chr11:77087200-77090600	Strong transcription	Rectal Mucosa Donor 31	rectum

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