Variant report

Variant	rs310459
Chromosome Location	chr19:56114237-56114238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:55986046..55989016-chr19:56110567..56114260,3	K562	blood:
2	chr10:14564447..14565279-chr19:56114132..56114918,2	MCF-7	breast:
3	chr19:56109378..56114662-chr19:56134412..56139001,15	K562	blood:
4	chr19:56113112..56115949-chr19:56151962..56154337,3	K562	blood:
5	chr19:56113470..56115355-chr20:55332546..55335378,2	MCF-7	breast:
6	chr19:55814981..55816687-chr19:56113260..56115264,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173581	Chromatin interaction
ENSG00000160469	Chromatin interaction
ENSG00000197483	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000269859	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1423053	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1423054	0.92[ASN][1000 genomes]
rs2902749	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs310458	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310460	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310461	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310462	0.97[ASN][1000 genomes]
rs497264	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs498199	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs609075	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
12	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
13	nsv912502	chr19:56099884-56138575	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56111600-56116000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:56112200-56116000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:56112400-56114600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:56112400-56114600	Enhancers	Gastric	stomach
5	chr19:56112400-56116000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:56112400-56116000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:56112400-56116400	Weak transcription	Aorta	Aorta
8	chr19:56112600-56115000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr19:56112600-56115400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr19:56112600-56116000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr19:56112600-56116000	Weak transcription	Fetal Lung	lung
12	chr19:56112600-56116000	Weak transcription	HSMMtube	muscle
13	chr19:56112800-56114600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:56112800-56114600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr19:56112800-56114600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr19:56112800-56114800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr19:56112800-56114800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:56112800-56115400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr19:56112800-56115400	Weak transcription	Fetal Intestine Large	intestine
20	chr19:56112800-56115600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr19:56112800-56115800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:56112800-56115800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr19:56112800-56115800	Weak transcription	Adipose Nuclei	Adipose
24	chr19:56112800-56115800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:56112800-56115800	Weak transcription	Fetal Brain Male	brain
26	chr19:56112800-56115800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr19:56112800-56115800	Weak transcription	HSMM	muscle
28	chr19:56112800-56116000	Weak transcription	Brain Angular Gyrus	brain
29	chr19:56112800-56116000	Weak transcription	Brain Anterior Caudate	brain
30	chr19:56112800-56116000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr19:56112800-56116000	Weak transcription	Fetal Kidney	kidney
32	chr19:56112800-56116000	Weak transcription	Left Ventricle	heart
33	chr19:56112800-56116000	Weak transcription	Psoas Muscle	Psoas
34	chr19:56112800-56116000	Weak transcription	Right Atrium	heart
35	chr19:56112800-56116000	Weak transcription	NH-A	brain
36	chr19:56113000-56114400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr19:56113000-56114600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr19:56113000-56114800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr19:56113000-56114800	Weak transcription	Dnd41	blood
40	chr19:56113000-56114800	Weak transcription	Hela-S3	cervix
41	chr19:56113000-56115000	Weak transcription	Primary B cells from cord blood	blood
42	chr19:56113000-56115200	Weak transcription	Fetal Brain Female	brain
43	chr19:56113000-56115400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr19:56113000-56115400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:56113000-56115400	Weak transcription	Liver	Liver
46	chr19:56113000-56115400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr19:56113000-56115800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr19:56113000-56115800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr19:56113000-56115800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:56113000-56115800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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