Variant report

Variant	rs11631118
Chromosome Location	chr15:51633396-51633397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:51633341-51634516	MCF-7	breast:	n/a	n/a
2	GATA2	chr15:51633053-51634214	SH-SY5Y	brain:	n/a	n/a
3	GATA3	chr15:51632850-51634260	MCF-7	breast:	n/a	n/a
4	MYC	chr15:51633350-51634421	MCF-7	breast:	n/a	chr15:51633425-51633436 chr15:51633425-51633436
5	MAX	chr15:51633303-51634618	H1-hESC	embryonic stem cell:	n/a	chr15:51633425-51633436 chr15:51633425-51633436
6	HDAC2	chr15:51633297-51634719	MCF-7	breast:	n/a	n/a
7	NR2F2	chr15:51633184-51634524	MCF-7	breast:	n/a	n/a
8	HA-E2F1	chr15:51633139-51634630	MCF-7	breast:	n/a	n/a
9	MAX	chr15:51633115-51634476	MCF-7	breast:	n/a	chr15:51633425-51633436 chr15:51633425-51633436
10	MAX	chr15:51633109-51634777	MCF-7	breast:	n/a	chr15:51633425-51633436 chr15:51633425-51633436

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:51633381-51633431	SAEC	small airway:	n/a
2	chr15:51633381-51633431	HRE	kidney:	n/a
3	chr15:51633381-51633431	NH-A	brain:	n/a
4	chr15:51633381-51633431	GM12892	blood:	n/a
5	chr15:51633381-51633431	PFSK-1	brain:	n/a
6	chr15:51633381-51633431	HCM	heart:	n/a
7	chr15:51633381-51633431	HUVEC	blood vessel:	n/a
8	chr15:51633381-51633431	ECC-1	luminal epithelium:	n/a
9	chr15:51633381-51633431	SKMC	muscle:	n/a
10	chr15:51633381-51633431	HMEC	breast:	n/a
11	chr15:51633381-51633431	SK-N-SH_RA	brain:	n/a
12	chr15:51633381-51633431	AG09309	skin:	n/a
13	chr15:51633381-51633431	HRPEpiC	eye:	n/a
14	chr15:51633381-51633431	K562	blood:	n/a
15	chr15:51633381-51633431	MCF-7	breast:	n/a
16	chr15:51633381-51633431	AG04450	lung:	fetal
17	chr15:51633381-51633431	SK-N-SH	brain:	n/a
18	chr15:51633381-51633431	AG10803	skin:	n/a
19	chr15:51633381-51633431	AG09319	gingival:	n/a
20	chr15:51633381-51633431	GM06990	blood:	n/a
21	chr15:51633381-51633431	HIPEpiC	eye:	n/a
22	chr15:51633381-51633431	PANC-1	pancreas:	n/a
23	chr15:51633381-51633431	NHDF-neo	bronchial:	n/a
24	chr15:51633381-51633431	NB4	blood:	n/a
25	chr15:51633381-51633431	HepG2	liver:	n/a
26	chr15:51633381-51633431	IMR90	lung:	fetal
27	chr15:51633381-51633431	LNCaP	prostate:	n/a
28	chr15:51633381-51633431	HCF	heart:	n/a
29	chr15:51633381-51633431	SK-N-MC	brain:	n/a
30	chr15:51633381-51633431	A549	lung:	n/a
31	chr15:51633381-51633431	HAEpiC	amniotic membrane:	n/a
32	chr15:51633381-51633431	HCT-116	colon:	n/a
33	chr15:51633381-51633431	ProgFib	skin:	n/a
34	chr15:51633381-51633431	PrEC	prostate:	n/a
35	chr15:51633381-51633431	AoSMC	blood vessel:	n/a
36	chr15:51633381-51633431	BE2_C	brain:	n/a
37	chr15:51633381-51633431	T-47D	breast:	n/a
38	chr15:51633381-51633431	HEEpiC	esophagus:	n/a
39	chr15:51633381-51633431	AG04449	skin:	fetal
40	chr15:51633381-51633431	HPAEpiC	pulmonary alveolar:	n/a
41	chr15:51633381-51633431	CMK	blood:	n/a
42	chr15:51633381-51633431	GM12891	blood:	n/a
43	chr15:51633381-51633431	RPTEC	kidney:	n/a
44	chr15:51633381-51633431	HL-60	blood:	n/a
45	chr15:51633381-51633431	HNPCEpiC	eye:	n/a
46	chr15:51633381-51633431	NT2-D1	testis:	n/a
47	chr15:51633381-51633431	NHBE	bronchial:	n/a
48	chr15:51633381-51633431	H1-hESC	embryonic stem cell:	embryo
49	chr15:51633381-51633431	BJ	skin:	n/a
50	chr15:51633381-51633431	HEK293	kidney:	embryo

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

No.	Distal block	Cell Line	Cell type
1	chr15:51631962..51635284-chr15:51658030..51661576,5	MCF-7	breast:
2	chr15:51629923..51631751-chr15:51631879..51634512,2	MCF-7	breast:
3	chr15:51633014..51633734-chr15:51672778..51673632,2	MCF-7	breast:
4	chr15:51632518..51637077-chr15:51639957..51644018,8	MCF-7	breast:

No data

Variant related genes	Relation type
CYP19A1	TF binding region
GLDN	TF binding region
CYP19A1	CpG island
GLDN	CpG island
ENSG00000270378	Chromatin interaction
ENSG00000137869	Chromatin interaction
ENSG00000259194	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1071955	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070842	0.80[AFR][1000 genomes]
rs11070843	0.89[ASW][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070844	0.82[MEX][hapmap];0.87[MKK][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070845	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630919	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632571	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12101686	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440754	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12441382	0.89[ASW][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12441859	0.89[ASW][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12592797	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12595133	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12595379	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1551656	0.82[MEX][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1870049	0.82[MEX][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1961177	0.82[MEX][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2445765	1.00[ASW][hapmap];0.96[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2445773	0.85[AFR][1000 genomes]
rs28500524	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493495	0.80[ASW][hapmap];0.86[MKK][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6493497	0.82[MEX][hapmap];0.92[MKK][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167696	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7175922	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7176005	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178417	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8027683	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031112	0.82[MEX][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8031184	0.82[MEX][hapmap];0.97[EUR][1000 genomes];0.91[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	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv904215	chr15:51542193-51673125	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv904216	chr15:51631479-51739808	Bivalent Enhancer Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11631118	GLDN	cis	Muscle Skeletal	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51628400-51633400	Weak transcription	Adipose Nuclei	Adipose
2	chr15:51628800-51633600	Weak transcription	Aorta	Aorta
3	chr15:51628800-51633600	Weak transcription	Right Atrium	heart
4	chr15:51630200-51633400	Weak transcription	Pancreas	Pancrea
5	chr15:51630800-51633600	Enhancers	Placenta	Placenta
6	chr15:51632200-51633600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:51632800-51633800	Enhancers	Spleen	Spleen
8	chr15:51633000-51633400	Enhancers	Brain Angular Gyrus	brain
9	chr15:51633000-51633400	Enhancers	Right Ventricle	heart
10	chr15:51633000-51633400	Enhancers	Stomach Smooth Muscle	stomach
11	chr15:51633000-51633800	Enhancers	Placenta Amnion	Placenta Amnion
12	chr15:51633200-51633400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
13	chr15:51633200-51633400	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr15:51633200-51633400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:51633200-51633400	Enhancers	Brain Substantia Nigra	brain
16	chr15:51633200-51633400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
17	chr15:51633200-51633400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
18	chr15:51633200-51633600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:51633200-51633600	Flanking Active TSS	Brain Cingulate Gyrus	brain
20	chr15:51633200-51633600	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr15:51633200-51633600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr15:51633200-51633600	Enhancers	Left Ventricle	heart
23	chr15:51633200-51633600	Enhancers	Psoas Muscle	Psoas
24	chr15:51633200-51633600	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
25	chr15:51633200-51634000	Bivalent Enhancer	Stomach Mucosa	stomach
26	chr15:51633200-51634200	Bivalent Enhancer	Primary B cells from peripheral blood	blood

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