Variant report

Variant	rs7129556
Chromosome Location	chr11:77300048-77300049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr11:77299807-77301958	MCF-7	breast:	n/a	n/a
2	POLR2A	chr11:77299923-77302161	HepG2	liver:	n/a	n/a
3	TCF7L2	chr11:77299802-77301737	PANC-1	pancreas:	n/a	n/a
4	MAX	chr11:77299984-77301900	MCF-7	breast:	n/a	n/a
5	MAX	chr11:77299950-77301749	A549	lung:	n/a	n/a
6	MAX	chr11:77299935-77301961	HepG2	liver:	n/a	n/a
7	MTA3	chr11:77300017-77300658	GM12878	blood:	n/a	n/a
8	BHLHE40	chr11:77300035-77301537	HepG2	liver:	n/a	n/a
9	POLR2A	chr11:77299934-77300139	ProgFib	skin:	n/a	n/a
10	MAX	chr11:77299930-77300769	Hela-S3	cervix:	n/a	n/a
11	JUN	chr11:77299908-77301340	K562	blood:	n/a	chr11:77300875-77300884
12	TCF7L2	chr11:77299798-77301226	Hela-S3	cervix:	n/a	n/a
13	E2F6	chr11:77299938-77301535	A549	lung:	n/a	chr11:77300876-77300885
14	POLR2A	chr11:77299805-77300114	Hela-S3	cervix:	n/a	n/a
15	MAX	chr11:77299967-77301380	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr11:77300002-77301305	K562	blood:	n/a	n/a
17	POLR2A	chr11:77300035-77301773	HepG2	liver:	n/a	n/a
18	POLR2A	chr11:77299928-77300100	K562	blood:	n/a	n/a
19	MAX	chr11:77299777-77301914	A549	lung:	n/a	n/a
20	POLR2A	chr11:77299910-77302030	HepG2	liver:	n/a	n/a
21	MAX	chr11:77299835-77301797	HepG2	liver:	n/a	n/a
22	MXI1	chr11:77299828-77302144	SK-N-SH	brain:	n/a	n/a
23	E2F6	chr11:77299936-77301655	H1-hESC	embryonic stem cell:	n/a	chr11:77300876-77300885

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:77300040..77302166-chr11:77305563..77307325,2	MCF-7	breast:
2	chr11:77299407..77303220-chr11:77304055..77306866,3	MCF-7	breast:
3	chr11:77276333..77280198-chr11:77299604..77302208,3	MCF-7	breast:
4	chr11:77299067..77304108-chr11:77304115..77308042,7	K562	blood:

No data

Variant related genes	Relation type
AQP11	TF binding region
ENSG00000271767	Chromatin interaction
ENSG00000238880	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10160677	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10793255	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10899386	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10899387	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10899389	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10899394	0.94[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11237215	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11237220	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11237225	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11237244	0.94[CEU][hapmap];0.94[CHD][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs11237246	0.81[EUR][1000 genomes]
rs11237249	1.00[CEU][hapmap];0.94[CHD][hapmap]
rs11512896	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11602520	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11823651	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12286317	0.80[GIH][hapmap]
rs2032395	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4509797	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs537811	0.80[GIH][hapmap]
rs650171	0.80[GIH][hapmap]
rs6592738	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72945508	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7927173	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv2752651	chr11:77211136-77318279	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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

Variant related diseases (count:1)

Disease	PMID	Source
Weight loss (gastric bypass surgery)	23643386	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7129556	MOGAT2	cis	parietal	SCAN
rs7129556	INTS4	cis	cerebellum	SCAN
rs7129556	AQP11	cis	parietal	SCAN
rs7129556	EDA2R	trans	parietal	SCAN
rs7129556	C11orf67	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77299400-77300200	Flanking Active TSS	Placenta	Placenta
2	chr11:77299600-77300400	Flanking Active TSS	Colonic Mucosa	Colon
3	chr11:77299600-77300600	Active TSS	Brain Germinal Matrix	brain
4	chr11:77299600-77300600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
5	chr11:77299600-77301000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr11:77299600-77301200	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr11:77299600-77302000	Active TSS	Pancreas	Pancrea
8	chr11:77299800-77300200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr11:77299800-77300200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:77299800-77300200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:77299800-77300200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr11:77299800-77300200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr11:77299800-77300200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:77299800-77300200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
15	chr11:77299800-77300200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr11:77299800-77300200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr11:77299800-77300200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr11:77299800-77300200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr11:77299800-77300200	Flanking Active TSS	Brain Angular Gyrus	brain
20	chr11:77299800-77300200	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr11:77299800-77300200	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr11:77299800-77300200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
23	chr11:77299800-77300200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr11:77299800-77300200	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr11:77299800-77300200	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr11:77299800-77300200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr11:77299800-77300200	Enhancers	Fetal Heart	heart
28	chr11:77299800-77300200	Flanking Active TSS	Fetal Intestine Large	intestine
29	chr11:77299800-77300200	Flanking Active TSS	Fetal Lung	lung
30	chr11:77299800-77300200	Flanking Active TSS	Fetal Muscle Trunk	muscle
31	chr11:77299800-77300200	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr11:77299800-77300200	Flanking Active TSS	Fetal Stomach	stomach
33	chr11:77299800-77300200	Flanking Active TSS	Ovary	ovary
34	chr11:77299800-77300200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr11:77299800-77300400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr11:77299800-77300400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr11:77299800-77300400	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr11:77299800-77300400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr11:77299800-77300400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr11:77299800-77300400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:77299800-77300400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:77299800-77300400	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr11:77299800-77300400	Flanking Active TSS	Liver	Liver
44	chr11:77299800-77300400	Flanking Active TSS	Fetal Intestine Small	intestine
45	chr11:77299800-77300400	Enhancers	Placenta Amnion	Placenta Amnion
46	chr11:77299800-77300400	Active TSS	Right Atrium	heart
47	chr11:77299800-77300400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr11:77299800-77300400	Flanking Active TSS	Stomach Smooth Muscle	stomach
49	chr11:77299800-77300400	Flanking Active TSS	HepG2	liver
50	chr11:77299800-77300400	Flanking Active TSS	HUVEC	blood vessel

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