Variant report

Variant	rs56084319
Chromosome Location	chr13:76110679-76110680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:76102775..76109881-chr13:76110381..76113047,9	MCF-7	breast:
2	chr13:76055919..76057695-chr13:76110507..76112437,2	MCF-7	breast:
3	chr13:76101020..76103303-chr13:76108939..76111291,2	K562	blood:
4	chr13:76109717..76113590-chr13:76122029..76126081,5	MCF-7	breast:
5	chr13:76109113..76111805-chr13:76112674..76114626,2	K562	blood:
6	chr13:76055248..76057886-chr13:76110224..76112780,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118939	Chromatin interaction
ENSG00000188243	Chromatin interaction
ENSG00000136111	Chromatin interaction
ENSG00000261553	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs4643195	0.97[ASN][1000 genomes]
rs4885306	0.93[ASN][1000 genomes]
rs4885308	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55983304	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60497706	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7321787	0.93[ASN][1000 genomes]
rs73223948	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73223955	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9543956	0.93[ASN][1000 genomes]
rs9543957	0.93[ASN][1000 genomes]
rs9543959	0.96[ASN][1000 genomes]
rs9573576	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9573577	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9573578	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761803	chr13:75943309-76161774	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv900562	chr13:76072743-76176680	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900563	chr13:76093935-76169347	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS 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 target site	12 gene(s)	inside rSNPs	diseases
4	nsv900564	chr13:76100090-76156136	Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	esv3326553	chr13:76106251-76120849	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3346687	chr13:76106451-76115149	Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv3363843	chr13:76106551-76113949	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv14404	chr13:76107773-76119573	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	esv2596575	chr13:76109159-76111338	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	esv1833250	chr13:76109534-76117768	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv442676	chr13:76109534-76117768	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	esv2760289	chr13:76109536-76117768	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	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
rs56084319	RP11-173B14.5	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76095800-76111400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:76096600-76111400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:76097000-76111000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr13:76097000-76111600	Weak transcription	Spleen	Spleen
5	chr13:76097800-76111200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr13:76098000-76111200	Weak transcription	Aorta	Aorta
7	chr13:76098600-76111000	Weak transcription	Colonic Mucosa	Colon
8	chr13:76098800-76111400	Weak transcription	Esophagus	oesophagus
9	chr13:76099600-76111000	Weak transcription	K562	blood
10	chr13:76100000-76111200	Weak transcription	Ovary	ovary
11	chr13:76103600-76111000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr13:76105000-76111200	Weak transcription	Stomach Mucosa	stomach
13	chr13:76107200-76110800	Strong transcription	Fetal Stomach	stomach
14	chr13:76107600-76111000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr13:76108000-76110800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr13:76108000-76111000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr13:76108400-76110800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:76108400-76110800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr13:76109000-76111000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr13:76109200-76111000	Enhancers	Primary T cells fromperipheralblood	blood
21	chr13:76109200-76111400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr13:76109400-76111000	Weak transcription	Placenta	Placenta
23	chr13:76109600-76110800	Enhancers	Primary T cells from cord blood	blood
24	chr13:76109600-76111000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr13:76109600-76111400	Weak transcription	Left Ventricle	heart
26	chr13:76109800-76110800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr13:76109800-76111000	Weak transcription	Fetal Lung	lung
28	chr13:76109800-76111200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr13:76109800-76111200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr13:76109800-76111400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr13:76109800-76111400	Weak transcription	Gastric	stomach
32	chr13:76109800-76111400	Weak transcription	Lung	lung
33	chr13:76110000-76110800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr13:76110000-76111000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr13:76110000-76111000	Genic enhancers	Fetal Muscle Leg	muscle
36	chr13:76110000-76111400	Enhancers	Small Intestine	intestine
37	chr13:76110200-76110800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr13:76110200-76110800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr13:76110200-76111000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr13:76110200-76111000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr13:76110200-76111000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr13:76110200-76111200	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr13:76110200-76111200	Enhancers	Colon Smooth Muscle	Colon
44	chr13:76110200-76111400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr13:76110400-76110800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr13:76110400-76110800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr13:76110400-76110800	Enhancers	Primary B cells from cord blood	blood
48	chr13:76110400-76110800	Genic enhancers	Primary hematopoietic stem cells	blood
49	chr13:76110400-76110800	Enhancers	Brain Cingulate Gyrus	brain
50	chr13:76110400-76110800	Transcr. at gene 5' and 3'	Dnd41	blood

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