Variant report

Variant	rs6509989
Chromosome Location	chr19:56815923-56815924
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56815074..56816909-chr19:56819293..56822091,2	K562	blood:
2	chr19:56815305..56818152-chr19:56824405..56826138,2	MCF-7	breast:
3	chr19:56782876..56785649-chr19:56814131..56816489,2	K562	blood:
4	chr19:56814154..56816778-chr19:56824607..56827217,3	K562	blood:
5	chr19:56815831..56819069-chr19:56823653..56827558,7	K562	blood:
6	chr19:56814282..56817166-chr19:56824782..56826304,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131848	Chromatin interaction
ENSG00000267298	Chromatin interaction
ENSG00000267710	Chromatin interaction
ENSG00000267549	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2304121	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[ASN][1000 genomes]
rs61351973	0.94[ASN][1000 genomes]
rs6509990	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73937232	0.96[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	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
2	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
3	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
4	nsv526325	chr19:56741186-56852035	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
7	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
8	nsv912517	chr19:56794645-56822466	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
10	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
11	nsv1058026	chr19:56799847-56833153	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56771400-56817200	Weak transcription	Fetal Brain Male	brain
2	chr19:56772800-56824200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr19:56779600-56820200	Weak transcription	Hela-S3	cervix
4	chr19:56782800-56825200	Weak transcription	Psoas Muscle	Psoas
5	chr19:56783000-56825000	Weak transcription	Stomach Mucosa	stomach
6	chr19:56785400-56823600	Weak transcription	Osteobl	bone
7	chr19:56788200-56824400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr19:56789000-56817400	Weak transcription	Small Intestine	intestine
9	chr19:56789000-56823800	Weak transcription	Brain Angular Gyrus	brain
10	chr19:56790600-56820000	Weak transcription	Primary B cells from cord blood	blood
11	chr19:56796400-56816600	Weak transcription	Fetal Kidney	kidney
12	chr19:56799800-56825200	Weak transcription	Right Atrium	heart
13	chr19:56800800-56817400	Weak transcription	Fetal Brain Female	brain
14	chr19:56802400-56821800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr19:56803000-56816600	Weak transcription	Dnd41	blood
16	chr19:56803000-56824200	Weak transcription	Fetal Thymus	thymus
17	chr19:56803200-56825000	Weak transcription	Colon Smooth Muscle	Colon
18	chr19:56803600-56816600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:56804400-56825000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr19:56804600-56825000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr19:56804800-56820200	Weak transcription	HSMM	muscle
22	chr19:56805200-56825400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:56805600-56820200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:56806000-56825000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:56806400-56816000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr19:56806400-56825200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:56806400-56825200	Weak transcription	Brain Hippocampus Middle	brain
28	chr19:56806400-56825200	Weak transcription	NH-A	brain
29	chr19:56806600-56825000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:56807000-56825200	Weak transcription	NHLF	lung
31	chr19:56807600-56823800	Weak transcription	GM12878-XiMat	blood
32	chr19:56807800-56825000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:56807800-56825200	Weak transcription	Brain Germinal Matrix	brain
34	chr19:56807800-56825200	Weak transcription	Colonic Mucosa	Colon
35	chr19:56807800-56825200	Weak transcription	Esophagus	oesophagus
36	chr19:56808200-56816600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:56808200-56821400	Weak transcription	Fetal Intestine Large	intestine
38	chr19:56808200-56825000	Weak transcription	HMEC	breast
39	chr19:56809200-56816600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:56810000-56825200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr19:56811200-56817600	Strong transcription	Liver	Liver
42	chr19:56813000-56816400	Strong transcription	Fetal Intestine Small	intestine
43	chr19:56813000-56817600	Strong transcription	Stomach Smooth Muscle	stomach
44	chr19:56813200-56816600	Weak transcription	Fetal Lung	lung
45	chr19:56813200-56816800	Strong transcription	Fetal Stomach	stomach
46	chr19:56813200-56817000	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr19:56813200-56817600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:56813200-56817800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr19:56813200-56822000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr19:56813400-56817600	Strong transcription	Pancreas	Pancrea

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