Variant report

Variant	rs538884
Chromosome Location	chr13:76334040-76334041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:76333862-76334065	ProgFib	skin:	n/a	n/a
2	TCF7L2	chr13:76333943-76335013	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr13:76334039-76337931	MCF10A-Er-Src	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:76334039-76334089	GM12878	blood:	n/a
2	chr13:76334039-76334089	Hela-S3	cervix:	n/a
3	chr13:76334039-76334089	HAEpiC	amniotic membrane:	n/a
4	chr13:76334039-76334089	SAEC	small airway:	n/a
5	chr13:76334039-76334089	IMR90	lung:	fetal
6	chr13:76334039-76334089	GM06990	blood:	n/a
7	chr13:76334039-76334089	SK-N-SH	brain:	n/a
8	chr13:76334039-76334089	T-47D	breast:	n/a
9	chr13:76334039-76334089	LNCaP	prostate:	n/a
10	chr13:76334039-76334089	AG04450	lung:	fetal
11	chr13:76334039-76334089	SKMC	muscle:	n/a
12	chr13:76334039-76334089	HUVEC	blood vessel:	n/a
13	chr13:76334039-76334089	MCF10A-Er-Src	breast:	n/a
14	chr13:76334039-76334089	HRCEpiC	kidney:	n/a
15	chr13:76334039-76334089	MCF-7	breast:	n/a
16	chr13:76334039-76334089	Caco-2	colon:	n/a
17	chr13:76334039-76334089	AG09319	gingival:	n/a
18	chr13:76334039-76334089	SK-N-MC	brain:	n/a
19	chr13:76334039-76334089	GM12891	blood:	n/a
20	chr13:76334039-76334089	HCF	heart:	n/a
21	chr13:76334039-76334089	Jurkat	blood:	n/a
22	chr13:76334039-76334089	HCT-116	colon:	n/a
23	chr13:76334039-76334089	Hepatocyte	liver:	n/a
24	chr13:76334039-76334089	HNPCEpiC	eye:	n/a
25	chr13:76334039-76334089	GM12892	blood:	n/a
26	chr13:76334039-76334089	NB4	blood:	n/a
27	chr13:76334039-76334089	PANC-1	pancreas:	n/a
28	chr13:76334039-76334089	NHBE	bronchial:	n/a
29	chr13:76334039-76334089	K562	blood:	n/a
30	chr13:76334039-76334089	BJ	skin:	n/a
31	chr13:76334039-76334089	HCM	heart:	n/a
32	chr13:76334039-76334089	U87	brain:	n/a
33	chr13:76334039-76334089	AG09309	skin:	n/a
34	chr13:76334039-76334089	AG04449	skin:	fetal
35	chr13:76334039-76334089	SK-N-SH_RA	brain:	n/a
36	chr13:76334039-76334089	HIPEpiC	eye:	n/a
37	chr13:76334039-76334089	ProgFib	skin:	n/a
38	chr13:76334039-76334089	ECC-1	luminal epithelium:	n/a
39	chr13:76334039-76334089	AG10803	skin:	n/a
40	chr13:76334039-76334089	NT2-D1	testis:	n/a
41	chr13:76334039-76334089	CMK	blood:	n/a
42	chr13:76334039-76334089	HRE	kidney:	n/a
43	chr13:76334039-76334089	AoSMC	blood vessel:	n/a
44	chr13:76334039-76334089	HEEpiC	esophagus:	n/a
45	chr13:76334039-76334089	NH-A	brain:	n/a
46	chr13:76334039-76334089	HepG2	liver:	n/a
47	chr13:76334039-76334089	BE2_C	brain:	n/a
48	chr13:76334039-76334089	HEK293	kidney:	embryo
49	chr13:76334039-76334089	PFSK-1	brain:	n/a
50	chr13:76334039-76334089	HMEC	breast:	n/a

No data

Variant related genes	Relation type
LMO7	TF binding region
LMO7	CpG island

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs2585628	1.00[AMR][1000 genomes]
rs2761075	1.00[AMR][1000 genomes]
rs2761076	1.00[AMR][1000 genomes]
rs486860	1.00[AMR][1000 genomes]
rs516359	1.00[AMR][1000 genomes]
rs525890	1.00[AMR][1000 genomes]
rs527890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs545943	1.00[AMR][1000 genomes]
rs588500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs592466	1.00[AMR][1000 genomes]
rs594666	1.00[AMR][1000 genomes]
rs596473	1.00[AMR][1000 genomes]
rs605536	1.00[AMR][1000 genomes]
rs606853	1.00[AMR][1000 genomes]
rs619523	1.00[AMR][1000 genomes]
rs621351	1.00[AMR][1000 genomes]
rs624802	1.00[AMR][1000 genomes]
rs642894	1.00[AMR][1000 genomes]
rs645822	1.00[AMR][1000 genomes]
rs654431	1.00[AMR][1000 genomes]
rs696777	1.00[AMR][1000 genomes]
rs696778	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949152	chr13:76211453-76366622	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76308200-76345200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr13:76322400-76334800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr13:76323800-76336600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr13:76323800-76356600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:76324000-76335200	Weak transcription	NH-A	brain
6	chr13:76324200-76334800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:76325200-76335200	Weak transcription	Ovary	ovary
8	chr13:76326000-76334600	Weak transcription	Fetal Lung	lung
9	chr13:76329200-76335600	Weak transcription	Primary B cells from cord blood	blood
10	chr13:76330600-76334400	Genic enhancers	Osteobl	bone
11	chr13:76330600-76334800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr13:76331400-76334600	Enhancers	NHDF-Ad	bronchial
13	chr13:76331800-76334600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr13:76332000-76334200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr13:76332000-76334400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr13:76332000-76336600	Weak transcription	Small Intestine	intestine
17	chr13:76332200-76334200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr13:76332200-76334400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr13:76332400-76334600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr13:76332600-76334400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr13:76333200-76334200	Enhancers	Fetal Intestine Large	intestine
22	chr13:76333400-76334200	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr13:76333600-76334400	Enhancers	Liver	Liver
24	chr13:76333600-76334800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr13:76333600-76338800	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr13:76333800-76334200	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr13:76333800-76334200	Enhancers	Esophagus	oesophagus
28	chr13:76333800-76334200	Flanking Active TSS	Stomach Mucosa	stomach
29	chr13:76333800-76334200	Enhancers	A549	lung
30	chr13:76333800-76334400	Enhancers	Pancreas	Pancrea
31	chr13:76333800-76334400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr13:76333800-76334400	Enhancers	Thymus	Thymus
33	chr13:76333800-76334400	Flanking Active TSS	Hela-S3	cervix
34	chr13:76333800-76334600	Flanking Active TSS	Fetal Intestine Small	intestine
35	chr13:76333800-76334600	Genic enhancers	HSMM	muscle
36	chr13:76333800-76334600	Enhancers	HSMMtube	muscle
37	chr13:76333800-76334800	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr13:76333800-76334800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr13:76333800-76334800	Enhancers	GM12878-XiMat	blood
40	chr13:76333800-76335000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr13:76333800-76335400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr13:76333800-76337800	Active TSS	Rectal Smooth Muscle	rectum
43	chr13:76334000-76334200	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr13:76334000-76334200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr13:76334000-76334200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr13:76334000-76334200	Flanking Active TSS	Fetal Brain Male	brain
47	chr13:76334000-76334200	Enhancers	Psoas Muscle	Psoas
48	chr13:76334000-76334200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr13:76334000-76334200	Flanking Bivalent TSS/Enh	HepG2	liver
50	chr13:76334000-76334400	Enhancers	Primary T cells from cord blood	blood

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