Variant report

Variant	rs10899398
Chromosome Location	chr11:77379099-77379100
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77377396..77379396-chr11:77381903..77384693,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10698394	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10793262	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10793263	0.86[ASN][1000 genomes]
rs10793264	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10899402	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899403	1.00[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10899405	1.00[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10899406	1.00[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10899407	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10899408	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899409	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11237284	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11237289	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11237295	1.00[ASW][hapmap];0.90[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11237299	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11237303	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11518811	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12222530	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12364072	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12794428	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1613945	0.83[EUR][1000 genomes]
rs1783546	0.81[EUR][1000 genomes]
rs1790240	0.81[EUR][1000 genomes]
rs1790246	1.00[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs1793341	0.81[EUR][1000 genomes]
rs2013296	0.84[CHB][hapmap];0.93[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap]
rs2212317	1.00[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298819	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2510967	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4245453	0.81[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4638330	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4945179	0.82[CHB][hapmap]
rs4945198	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4945199	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4945201	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4945206	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs496786	1.00[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs574665	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61900164	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6592741	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap]
rs7110924	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7115612	0.81[MEX][hapmap]
rs7128224	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7130719	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7358471	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7925343	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7927913	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7931272	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7940734	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7946637	0.84[CHB][hapmap];0.93[LWK][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap]
rs9666484	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9988883	1.00[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1038974	chr11:77284036-77431228	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1041384	chr11:77284558-77419809	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1048892	chr11:77290458-77431228	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv1053074	chr11:77290458-77435831	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv468641	chr11:77301341-77420314	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	nsv555452	chr11:77301341-77420314	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv1035494	chr11:77309696-77431228	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10899398	PAK1	cis	cerebellum	SCAN
rs10899398	AQP11	cis	parietal	SCAN
rs10899398	INTS4	cis	cerebellum	SCAN
rs10899398	INTS4	cis	parietal	SCAN
rs10899398	INT4	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77360400-77419200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:77370000-77410400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:77370200-77380200	Weak transcription	NHDF-Ad	bronchial
4	chr11:77373400-77381200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr11:77373800-77379800	Strong transcription	HSMM	muscle
6	chr11:77373800-77413600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:77374000-77416200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:77374200-77417400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr11:77374400-77382800	Weak transcription	Psoas Muscle	Psoas
10	chr11:77374800-77414000	Strong transcription	Fetal Thymus	thymus
11	chr11:77375000-77380000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:77375000-77390200	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr11:77375000-77411200	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr11:77375000-77411200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr11:77375000-77413000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr11:77375200-77380000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:77375200-77387800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:77375200-77411000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr11:77375200-77411000	Strong transcription	Liver	Liver
20	chr11:77375200-77413600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:77375400-77387200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:77375400-77387400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr11:77375400-77389800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr11:77375400-77389800	Strong transcription	Placenta	Placenta
25	chr11:77375400-77390000	Strong transcription	Adipose Nuclei	Adipose
26	chr11:77375400-77391200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr11:77375400-77394600	Strong transcription	Fetal Muscle Leg	muscle
28	chr11:77375400-77395400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:77375400-77396400	Strong transcription	Primary hematopoietic stem cells	blood
30	chr11:77375400-77404800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:77375400-77411000	Strong transcription	Dnd41	blood
32	chr11:77375600-77381600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:77375600-77387400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr11:77375600-77390200	Strong transcription	Primary B cells from cord blood	blood
35	chr11:77375600-77395200	Strong transcription	Primary T cells from cord blood	blood
36	chr11:77375600-77395800	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr11:77375600-77405000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:77375600-77411200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr11:77375600-77413200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr11:77375600-77413400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:77375800-77380600	Strong transcription	GM12878-XiMat	blood
42	chr11:77375800-77404800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr11:77376200-77394800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:77376400-77379800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr11:77376400-77388400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:77376600-77380000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr11:77376600-77388000	Strong transcription	Stomach Smooth Muscle	stomach
48	chr11:77376800-77415600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr11:77377000-77379800	Weak transcription	Small Intestine	intestine
50	chr11:77377000-77380000	Weak transcription	Fetal Heart	heart

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