Variant report

Variant	rs488196
Chromosome Location	chr19:56677299-56677300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56673116..56675836-chr19:56676117..56678644,2	K562	blood:
2	chr19:56670800..56672784-chr19:56675448..56678240,2	MCF-7	breast:
3	chr19:56671026..56674616-chr19:56677144..56679269,3	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs16987029	0.89[JPT][hapmap]
rs16987031	0.89[JPT][hapmap]
rs2631642	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631652	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs274141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs274144	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs274145	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs274146	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs274151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs274154	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs274155	0.83[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs274156	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs274159	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs274163	1.00[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs274165	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs274167	0.87[EUR][1000 genomes]
rs274168	0.90[CEU][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap]
rs274180	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs274182	1.00[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3103059	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3103060	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs480528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs481291	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs482506	0.97[ASN][1000 genomes]
rs487922	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488118	0.97[ASN][1000 genomes]
rs565171	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs581486	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61283021	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs650832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs651800	0.97[ASN][1000 genomes]
rs652204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671061	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs672956	0.89[ASN][1000 genomes]
rs679082	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs901476	1.00[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][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	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
10	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
11	nsv528361	chr19:56638845-56688570	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56654000-56681600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:56670200-56678000	Weak transcription	HepG2	liver
3	chr19:56670800-56681600	Weak transcription	A549	lung
4	chr19:56670800-56681800	Weak transcription	NHEK	skin
5	chr19:56671600-56683200	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr19:56672200-56683200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr19:56672400-56683200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr19:56672600-56678800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr19:56672600-56681200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:56672600-56681800	Weak transcription	Ovary	ovary
11	chr19:56672600-56684200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr19:56672600-56685600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:56672800-56681200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr19:56672800-56681600	Weak transcription	Esophagus	oesophagus
15	chr19:56672800-56683200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:56672800-56683200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr19:56672800-56683400	Weak transcription	Fetal Intestine Large	intestine
18	chr19:56673000-56690000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:56673200-56678200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:56673200-56678200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:56673200-56681800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:56673200-56681800	Weak transcription	Adipose Nuclei	Adipose
23	chr19:56673200-56683200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:56673200-56683200	Weak transcription	Fetal Muscle Leg	muscle
25	chr19:56673400-56681600	Weak transcription	Pancreas	Pancrea
26	chr19:56673400-56683200	Weak transcription	Liver	Liver
27	chr19:56673600-56683200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr19:56673800-56681600	Weak transcription	Spleen	Spleen
29	chr19:56673800-56683200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr19:56674000-56678000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr19:56674200-56677400	Weak transcription	Brain Germinal Matrix	brain
32	chr19:56674400-56683200	Weak transcription	Fetal Stomach	stomach
33	chr19:56674800-56681800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:56675600-56683200	Weak transcription	Primary B cells from peripheral blood	blood

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