Variant report

Variant	rs55664539
Chromosome Location	chr13:95253327-95253328
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	NFYB	chr13:95253241-95253441	GM12878	blood:	n/a	chr13:95253350-95253363
2	JUN	chr13:95253041-95254653	K562	blood:	n/a	chr13:95253498-95253507 chr13:95253495-95253504 chr13:95254099-95254108 chr13:95253496-95253505 chr13:95253494-95253503 chr13:95253497-95253506 chr13:95253492-95253501
3	E2F6	chr13:95253255-95254708	H1-hESC	embryonic stem cell:	n/a	chr13:95254335-95254344 chr13:95254130-95254140 chr13:95253532-95253541 chr13:95254137-95254147 chr13:95253880-95253891 chr13:95254335-95254347 chr13:95254098-95254107
4	ELK1	chr13:95253180-95253346	Hela-S3	cervix:	n/a	n/a
5	E2F6	chr13:95253123-95254820	H1-hESC	embryonic stem cell:	n/a	chr13:95254335-95254344 chr13:95254130-95254140 chr13:95253532-95253541 chr13:95254137-95254147 chr13:95253880-95253891 chr13:95254335-95254347 chr13:95254098-95254107
6	POLR2A	chr13:95253289-95254685	MCF10A-Er-Src	breast:	n/a	n/a
7	MAX	chr13:95253211-95253357	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:95200950..95203234-chr13:95251840..95253410,2	MCF-7	breast:
2	chr13:95247274..95249727-chr13:95251841..95255221,4	MCF-7	breast:
3	chr13:95245952..95249992-chr13:95252491..95255739,5	K562	blood:
4	chr13:95246267..95250128-chr13:95251933..95256020,6	MCF-7	breast:

Variant related genes	Relation type
TGDS	TF binding region
GPR180	TF binding region
ENSG00000088451	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11839030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12100288	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12100322	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12100358	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56730982	1.00[EUR][1000 genomes]
rs74104485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7992666	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34004	chr13:94906537-95392644	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription 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 target site	27 gene(s)	inside rSNPs	diseases
2	nsv832685	chr13:95179676-95279966	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv832686	chr13:95206742-95400992	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv19608	chr13:95253055-95253914	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv821089	chr13:95253055-95253914	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95248800-95253600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr13:95248800-95253600	Weak transcription	HUVEC	blood vessel
3	chr13:95249000-95253600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr13:95249000-95253600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr13:95249000-95253600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr13:95249000-95253600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr13:95249000-95253600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr13:95249000-95253600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr13:95249000-95253600	Weak transcription	Adipose Nuclei	Adipose
10	chr13:95249000-95253600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr13:95249000-95253600	Weak transcription	Right Atrium	heart
12	chr13:95249000-95253600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr13:95249000-95253800	Weak transcription	Spleen	Spleen
14	chr13:95249200-95253600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr13:95249200-95253600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr13:95249200-95253600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr13:95249200-95253600	Weak transcription	Colonic Mucosa	Colon
18	chr13:95249200-95253600	Weak transcription	NHEK	skin
19	chr13:95250600-95253600	Weak transcription	NHLF	lung
20	chr13:95251000-95253600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr13:95252000-95253400	Enhancers	Stomach Mucosa	stomach
22	chr13:95252000-95253600	Enhancers	Fetal Intestine Large	intestine
23	chr13:95252200-95253600	Enhancers	Liver	Liver
24	chr13:95252400-95253600	Enhancers	Duodenum Mucosa	Duodenum
25	chr13:95252800-95253400	ZNF genes & repeats	GM12878-XiMat	blood
26	chr13:95252800-95253600	Enhancers	Primary B cells from peripheral blood	blood
27	chr13:95253000-95253600	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr13:95253000-95253600	Enhancers	Fetal Muscle Leg	muscle
29	chr13:95253000-95253600	Enhancers	Dnd41	blood
30	chr13:95253000-95253600	Weak transcription	HMEC	breast
31	chr13:95253000-95255600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr13:95253200-95253400	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr13:95253200-95253400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr13:95253200-95253400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr13:95253200-95253400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr13:95253200-95253400	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr13:95253200-95253400	Flanking Active TSS	Colon Smooth Muscle	Colon
38	chr13:95253200-95253400	Flanking Active TSS	Fetal Kidney	kidney
39	chr13:95253200-95253400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr13:95253200-95253400	Flanking Active TSS	Osteobl	bone
41	chr13:95253200-95253600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr13:95253200-95253600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr13:95253200-95253600	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr13:95253200-95253600	Weak transcription	Primary B cells from cord blood	blood
45	chr13:95253200-95253600	Enhancers	Primary T cells from cord blood	blood
46	chr13:95253200-95253600	Enhancers	Primary T cells fromperipheralblood	blood
47	chr13:95253200-95253600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr13:95253200-95253600	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr13:95253200-95253600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr13:95253200-95253600	Enhancers	Primary T helper cells PMA-I stimulated	--

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