Variant report

Variant	rs16984438
Chromosome Location	chr19:53598829-53598830
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:53592779..53599104-chr19:53601029..53609520,13	K562	blood:
2	chr19:53586275..53589046-chr19:53598456..53600578,2	K562	blood:
3	chr19:53592480..53599104-chr19:53600939..53607737,12	K562	blood:
4	chr19:53598253..53601018-chr19:53604672..53606722,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170949	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10402901	1.00[CHB][hapmap]
rs10406237	1.00[CHB][hapmap];0.92[MKK][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs10409615	1.00[ASN][1000 genomes]
rs10410030	1.00[CHB][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs10412805	1.00[ASN][1000 genomes]
rs10418505	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12971916	1.00[CHB][hapmap]
rs12982323	1.00[CHB][hapmap]
rs1661923	1.00[CHB][hapmap]
rs16984443	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16984486	1.00[CHB][hapmap];0.81[YRI][hapmap];1.00[ASN][1000 genomes]
rs28368410	1.00[ASN][1000 genomes]
rs28528321	1.00[ASN][1000 genomes]
rs28661145	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28662846	1.00[ASN][1000 genomes]
rs28691095	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28701520	1.00[ASN][1000 genomes]
rs28726276	1.00[ASN][1000 genomes]
rs58143828	1.00[ASN][1000 genomes]
rs6509725	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7247568	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7253566	1.00[ASN][1000 genomes]
rs73935216	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73935236	1.00[ASN][1000 genomes]
rs8099848	1.00[ASN][1000 genomes]
rs8100134	1.00[ASN][1000 genomes]
rs8102799	1.00[CHB][hapmap];0.92[MKK][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs8109900	1.00[CHB][hapmap]
rs8110394	1.00[CHB][hapmap]
rs8113824	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
10	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
12	nsv580068	chr19:53594806-53623771	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv912343	chr19:53594806-53632896	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv3374307	chr19:53597540-53599538	Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv3323019	chr19:53598040-53599038	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53573600-53604800	Weak transcription	Hela-S3	cervix
2	chr19:53574800-53599600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:53575600-53601000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr19:53576800-53605200	Weak transcription	Stomach Mucosa	stomach
5	chr19:53584000-53599000	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr19:53584600-53599400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr19:53584600-53599800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:53585200-53599400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr19:53585200-53599600	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr19:53585400-53604800	Weak transcription	Psoas Muscle	Psoas
11	chr19:53585600-53599000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:53585600-53599200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:53586000-53599000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:53586000-53599200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:53586000-53599600	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr19:53586400-53599400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:53586400-53599800	Strong transcription	Duodenum Mucosa	Duodenum
18	chr19:53586400-53603400	Strong transcription	Primary T cells from cord blood	blood
19	chr19:53586600-53599200	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr19:53586600-53599600	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr19:53586600-53600000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr19:53586800-53599600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:53588200-53601200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr19:53588400-53603400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr19:53588600-53599800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:53589200-53604800	Weak transcription	Fetal Brain Male	brain
27	chr19:53589600-53604800	Weak transcription	Small Intestine	intestine
28	chr19:53590200-53599600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr19:53590400-53605000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr19:53590600-53599000	Strong transcription	Fetal Muscle Leg	muscle
31	chr19:53591200-53599600	Genic enhancers	Fetal Intestine Large	intestine
32	chr19:53591800-53599200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:53592800-53604800	Weak transcription	HUVEC	blood vessel
34	chr19:53593400-53599600	ZNF genes & repeats	A549	lung
35	chr19:53594000-53599000	Strong transcription	K562	blood
36	chr19:53594400-53600600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr19:53594400-53601000	Weak transcription	Primary B cells from cord blood	blood
38	chr19:53594400-53603400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr19:53594400-53605200	Weak transcription	Fetal Lung	lung
40	chr19:53594600-53600800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr19:53594600-53604800	Weak transcription	Fetal Kidney	kidney
42	chr19:53594600-53604800	Weak transcription	NHEK	skin
43	chr19:53595000-53600000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:53595000-53600800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr19:53595000-53600800	Weak transcription	Colon Smooth Muscle	Colon
46	chr19:53595000-53600800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr19:53595000-53601000	Weak transcription	Aorta	Aorta
48	chr19:53595000-53601000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:53595000-53601000	Weak transcription	HMEC	breast
50	chr19:53595200-53600600	Weak transcription	Adipose Nuclei	Adipose

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