Variant report

Variant	rs4802588
Chromosome Location	chr19:39030132-39030133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39028104..39030194-chr19:39213842..39216117,2	K562	blood:
2	chr19:39022005..39025490-chr19:39026869..39030422,4	K562	blood:
3	chr19:39029247..39031179-chr19:39031393..39034071,2	MCF-7	breast:
4	chr19:39028747..39031280-chr19:39032458..39034855,3	K562	blood:

Variant related genes	Relation type
ENSG00000196218	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1004795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1004796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10415792	0.88[EUR][1000 genomes]
rs12459024	1.00[ASN][1000 genomes]
rs12459749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462061	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984412	1.00[ASN][1000 genomes]
rs2292797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960350	1.00[ASN][1000 genomes]
rs34754809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829976	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs45613041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802589	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802608	1.00[AFR][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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv911663	chr19:38899548-39101879	Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv833824	chr19:38914618-39084758	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1816081	chr19:38919971-39050479	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
8	nsv911664	chr19:38924814-39048163	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv911665	chr19:38924814-39101879	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS 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	37 gene(s)	inside rSNPs	diseases
11	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv1058902	chr19:39025940-39078574	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv1064490	chr19:39029788-39078574	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38960800-39034400	Strong transcription	Skeletal Muscle Female	skeletal muscle
2	chr19:38963000-39033000	Strong transcription	Skeletal Muscle Male	skeletal muscle
3	chr19:38985200-39081800	Weak transcription	Psoas Muscle	Psoas
4	chr19:39026000-39052400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:39026400-39030200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr19:39026400-39034200	Weak transcription	Brain Substantia Nigra	brain
7	chr19:39026400-39034400	Weak transcription	Brain Angular Gyrus	brain
8	chr19:39026400-39034800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr19:39026600-39034000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:39026600-39034400	Weak transcription	Brain Anterior Caudate	brain
11	chr19:39026600-39034400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr19:39026600-39034400	Weak transcription	Brain Hippocampus Middle	brain
13	chr19:39026600-39034400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:39026600-39034800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr19:39026600-39034800	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr19:39026800-39031600	Weak transcription	Right Atrium	heart
17	chr19:39027000-39031000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr19:39027200-39030800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr19:39027600-39030400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr19:39027800-39030200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:39027800-39030600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:39027800-39030600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr19:39027800-39034200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr19:39028200-39034200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:39028400-39030400	Enhancers	Brain Germinal Matrix	brain
26	chr19:39028400-39035200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:39028600-39034200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr19:39028600-39034800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr19:39028800-39030600	Enhancers	Adipose Nuclei	Adipose
30	chr19:39028800-39030800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:39029000-39030200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr19:39029000-39030200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr19:39029000-39051600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr19:39029200-39030200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr19:39029200-39030600	Genic enhancers	HSMMtube	muscle
36	chr19:39029200-39031800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:39029200-39034400	Weak transcription	Esophagus	oesophagus
38	chr19:39029200-39034400	Weak transcription	Pancreas	Pancrea
39	chr19:39029600-39030200	Enhancers	Stomach Mucosa	stomach
40	chr19:39029600-39030800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr19:39029600-39030800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr19:39029600-39030800	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr19:39029600-39046000	Weak transcription	HSMM	muscle
44	chr19:39029800-39030800	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr19:39029800-39030800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr19:39029800-39031200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr19:39029800-39034600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr19:39029800-39035000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:39029800-39035200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr19:39030000-39030800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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