Variant report

Variant	rs71368856
Chromosome Location	chr19:56087597-56087598
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56086664..56089219-chr19:56150784..56152646,2	MCF-7	breast:
2	chr19:56085801..56089181-chr19:56090146..56094195,5	MCF-7	breast:
3	chr19:55916968..55919550-chr19:56086420..56090390,4	K562	blood:
4	chr19:56087478..56090277-chr19:56092054..56093869,2	MCF-7	breast:
5	chr19:56087311..56094258-chr19:56108819..56113699,11	K562	blood:
6	chr19:55916968..55919340-chr19:56087208..56090390,3	K562	blood:

Variant related genes	Relation type
ENSG00000108106	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000218891	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000171425	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10403462	0.81[ASN][1000 genomes]
rs10451452	0.82[ASN][1000 genomes]
rs1079082	0.93[ASN][1000 genomes]
rs1079083	0.93[ASN][1000 genomes]
rs1079084	0.93[ASN][1000 genomes]
rs1079085	0.93[ASN][1000 genomes]
rs11084402	0.95[ASN][1000 genomes]
rs11665826	0.95[ASN][1000 genomes]
rs11668725	0.92[ASN][1000 genomes]
rs11668729	0.92[ASN][1000 genomes]
rs11669682	0.95[ASN][1000 genomes]
rs11879347	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12610510	0.99[ASN][1000 genomes]
rs12610512	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610709	0.93[ASN][1000 genomes]
rs12610881	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12972159	0.95[ASN][1000 genomes]
rs12974617	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12978375	0.92[ASN][1000 genomes]
rs12979354	0.95[ASN][1000 genomes]
rs12979366	0.95[ASN][1000 genomes]
rs12980543	0.95[ASN][1000 genomes]
rs2014329	0.91[ASN][1000 genomes]
rs2864433	0.95[ASN][1000 genomes]
rs2902748	0.95[ASN][1000 genomes]
rs34174244	0.95[ASN][1000 genomes]
rs34715654	0.86[ASN][1000 genomes]
rs34937940	0.99[ASN][1000 genomes]
rs35088354	0.86[ASN][1000 genomes]
rs35197282	0.95[ASN][1000 genomes]
rs35522245	0.95[ASN][1000 genomes]
rs35839536	0.95[ASN][1000 genomes]
rs36047579	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60220392	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71368855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246944	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7251733	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer 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	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv912495	chr19:56033088-56132661	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers 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	49 gene(s)	inside rSNPs	diseases
6	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
9	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS 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	67 gene(s)	inside rSNPs	diseases
10	nsv912499	chr19:56071293-56132487	Flanking Active TSS Genic enhancers Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56067400-56088400	Weak transcription	Gastric	stomach
2	chr19:56075600-56087600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr19:56075800-56090400	Weak transcription	Psoas Muscle	Psoas
4	chr19:56076000-56088200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr19:56076000-56088200	Weak transcription	Left Ventricle	heart
6	chr19:56076000-56088400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr19:56076000-56091000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr19:56076000-56091000	Weak transcription	Right Atrium	heart
9	chr19:56076400-56088200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr19:56076400-56088600	Weak transcription	Colonic Mucosa	Colon
11	chr19:56076600-56091000	Weak transcription	Fetal Heart	heart
12	chr19:56078600-56091000	Weak transcription	Fetal Kidney	kidney
13	chr19:56081000-56088200	Weak transcription	NHLF	lung
14	chr19:56081200-56088800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr19:56081800-56091000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr19:56082200-56088800	Weak transcription	Pancreas	Pancrea
17	chr19:56082400-56088200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr19:56082600-56087600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:56083400-56087600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:56083800-56088400	Weak transcription	Spleen	Spleen
21	chr19:56083800-56091000	Weak transcription	HepG2	liver
22	chr19:56084000-56087600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:56084200-56088200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:56084200-56091000	Weak transcription	K562	blood
25	chr19:56084400-56088200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:56084400-56088400	Weak transcription	Right Ventricle	heart
27	chr19:56085000-56087600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr19:56085000-56087600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:56085000-56088200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr19:56085200-56087600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr19:56085200-56087600	Weak transcription	Fetal Intestine Small	intestine
32	chr19:56085200-56087600	Weak transcription	Osteobl	bone
33	chr19:56085200-56088200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr19:56085200-56088400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:56085200-56090000	Weak transcription	Fetal Lung	lung
36	chr19:56085400-56087600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:56085400-56087600	Weak transcription	A549	lung
38	chr19:56085400-56088200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr19:56085600-56088000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr19:56085600-56088200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr19:56085600-56088800	Weak transcription	Brain Hippocampus Middle	brain
42	chr19:56085800-56087600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr19:56085800-56087600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr19:56085800-56088000	Weak transcription	Dnd41	blood
45	chr19:56085800-56088200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:56085800-56088200	Weak transcription	NHEK	skin
47	chr19:56086000-56088200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:56086000-56088200	Weak transcription	Adipose Nuclei	Adipose
49	chr19:56086000-56088400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr19:56086000-56090000	Weak transcription	Stomach Smooth Muscle	stomach

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