Variant report

Variant	rs11029779
Chromosome Location	chr11:3815536-3815537
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	POLR2A	chr11:3815383-3816213	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:3815253..3816914-chr11:3817016..3818903,2	MCF-7	breast:
2	chr11:3792691..3794199-chr11:3815236..3817396,2	MCF-7	breast:
3	chr11:3813727..3817050-chr11:3817081..3819482,4	K562	blood:

Variant related genes	Relation type
PGAP2	TF binding region
ENSG00000110713	Chromatin interaction
ENSG00000148985	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10835097	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs188044	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs190680	0.85[ASN][1000 genomes]
rs2599737	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2672219	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs276885	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs276889	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs276892	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs276895	0.87[ASN][1000 genomes]
rs276900	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs276903	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs276904	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs276905	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs276908	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs276909	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2943415	0.82[AMR][1000 genomes]
rs2957866	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2957872	0.83[ASN][1000 genomes]
rs598041	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs605177	0.80[ASN][1000 genomes]
rs623056	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs640359	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs658731	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs685537	0.85[ASN][1000 genomes]
rs7101445	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7119248	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7927587	0.87[EUR][1000 genomes]
rs7941146	0.88[ASN][1000 genomes]

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	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11029779	TMEM80	cis	parietal	SCAN
rs11029779	FAM99A	cis	parietal	SCAN
rs11029779	TMEM80	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3739400-3817600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:3780600-3817000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:3786800-3816000	Weak transcription	Stomach Mucosa	stomach
4	chr11:3793800-3816800	Weak transcription	Fetal Heart	heart
5	chr11:3793800-3817000	Weak transcription	Fetal Brain Male	brain
6	chr11:3800400-3816400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr11:3800400-3816400	Weak transcription	Small Intestine	intestine
8	chr11:3800400-3817000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:3800400-3817600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:3800600-3816400	Weak transcription	Colonic Mucosa	Colon
11	chr11:3800600-3817000	Weak transcription	HSMMtube	muscle
12	chr11:3800600-3817200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:3804600-3816000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:3805400-3816000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr11:3808400-3815800	Weak transcription	Brain Angular Gyrus	brain
16	chr11:3808400-3815800	Strong transcription	Fetal Thymus	thymus
17	chr11:3808400-3816400	Strong transcription	Fetal Stomach	stomach
18	chr11:3808400-3816600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr11:3808800-3815800	Weak transcription	Gastric	stomach
20	chr11:3808800-3815800	Weak transcription	Ovary	ovary
21	chr11:3808800-3815800	Weak transcription	Psoas Muscle	Psoas
22	chr11:3808800-3816600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr11:3808800-3816600	Weak transcription	NHLF	lung
24	chr11:3808800-3816800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:3808800-3817000	Weak transcription	NHDF-Ad	bronchial
26	chr11:3809000-3817200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr11:3810400-3816200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr11:3810600-3815800	Weak transcription	Primary B cells from cord blood	blood
29	chr11:3810800-3815600	Strong transcription	Fetal Muscle Leg	muscle
30	chr11:3810800-3816800	Strong transcription	Fetal Intestine Small	intestine
31	chr11:3811000-3816000	Strong transcription	Thymus	Thymus
32	chr11:3811000-3816200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:3811200-3815600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:3811200-3815600	Strong transcription	Lung	lung
35	chr11:3811200-3815800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:3811200-3816000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr11:3811200-3816000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr11:3811200-3816200	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr11:3811200-3816600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr11:3811200-3816800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr11:3811200-3816800	Strong transcription	Fetal Intestine Large	intestine
42	chr11:3811200-3817000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr11:3811400-3816200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:3811400-3816400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr11:3811600-3815800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:3811800-3816400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:3812000-3815600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr11:3812200-3815600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr11:3812200-3815800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:3812200-3816400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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