Variant report

Variant	rs59961449
Chromosome Location	chr19:18402050-18402051
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18400699..18403651-chr19:18419852..18422642,3	MCF-7	breast:
2	chr19:18312262..18317051-chr19:18400963..18403805,6	K562	blood:
3	chr19:18397375..18399268-chr19:18401136..18404109,3	MCF-7	breast:
4	chr19:18401578..18404276-chr19:18423557..18426532,3	MCF-7	breast:
5	chr19:18302170..18305660-chr19:18401195..18405858,4	K562	blood:
6	chr19:18401875..18403454-chr19:18498375..18500972,2	K562	blood:
7	chr19:18399894..18406849-chr19:18524216..18528146,7	K562	blood:
8	chr19:18401356..18404646-chr19:18426877..18430398,3	MCF-7	breast:
9	chr19:18400747..18403330-chr19:18449390..18451589,2	MCF-7	breast:
10	chr19:18401829..18404172-chr19:18534025..18536659,2	K562	blood:
11	chr19:18219734..18221957-chr19:18401756..18404165,2	K562	blood:
12	chr19:18401219..18403763-chr19:18495464..18498325,2	K562	blood:
13	chr19:18401175..18404023-chr19:18537863..18539807,2	K562	blood:
14	chr17:39844719..39845553-chr19:18401986..18402575,2	Hela-S3	cervix:
15	chr19:18383365..18408325-chr19:18518460..18533256,66	K562	blood:
16	chr19:18401391..18404924-chr19:18547602..18550007,3	K562	blood:
17	chr19:18399345..18407720-chr19:18430417..18436364,18	MCF-7	breast:
18	chr19:18401957..18405099-chr19:18441028..18445565,5	MCF-7	breast:
19	chr19:18397948..18402412-chr19:18484415..18487037,3	K562	blood:
20	chr19:18401371..18405274-chr19:18416257..18419267,5	MCF-7	breast:
21	chr15:99191395..99191979-chr19:18401624..18402537,2	Hela-S3	cervix:
22	chr19:18401679..18404402-chr19:18698590..18700226,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000006015	Chromatin interaction
ENSG00000268650	Chromatin interaction
ENSG00000105649	Chromatin interaction
ENSG00000130520	Chromatin interaction
ENSG00000239821	Chromatin interaction
ENSG00000105655	Chromatin interaction
ENSG00000221167	Chromatin interaction
ENSG00000264175	Chromatin interaction
ENSG00000099308	Chromatin interaction
ENSG00000130511	Chromatin interaction
ENSG00000173812	Chromatin interaction
ENSG00000130517	Chromatin interaction
ENSG00000130513	Chromatin interaction
ENSG00000254858	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1079165	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1079166	0.83[ASN][1000 genomes]
rs10854164	0.86[ASN][1000 genomes]
rs12459276	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12460547	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12461261	0.83[ASN][1000 genomes]
rs12461701	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12461751	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1421720	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1549143	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17711565	0.88[ASN][1000 genomes]
rs41347350	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41481544	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4808125	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4808778	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57090641	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58555271	0.84[EUR][1000 genomes]
rs60086589	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60170051	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62120437	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7247237	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7247767	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7248070	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8103549	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
5	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
6	nsv911269	chr19:18351674-18418044	Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
7	nsv911270	chr19:18351674-18422364	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
8	nsv911271	chr19:18362940-18453124	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
9	nsv828472	chr19:18377725-18404131	Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	117 gene(s)	inside rSNPs	diseases
10	esv1833305	chr19:18378219-18408222	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	117 gene(s)	inside rSNPs	diseases
11	nsv911272	chr19:18378219-18439383	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
12	nsv911273	chr19:18386798-18454825	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	134 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs59961449	KIAA1683	cis	Thyroid	GTEx
rs59961449	KIAA1683	cis	Skin Sun Exposed Lower leg	GTEx
rs59961449	KIAA1683	cis	Esophagus Muscularis	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18394000-18402800	Weak transcription	Gastric	stomach
2	chr19:18394600-18402200	Weak transcription	Psoas Muscle	Psoas
3	chr19:18396000-18402600	Weak transcription	Small Intestine	intestine
4	chr19:18396200-18402600	Weak transcription	Liver	Liver
5	chr19:18397800-18402200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:18398400-18402200	Enhancers	Fetal Thymus	thymus
7	chr19:18399400-18402200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:18399400-18402200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:18399400-18402200	Weak transcription	Fetal Kidney	kidney
10	chr19:18399400-18402400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:18399600-18402200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr19:18399600-18402200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:18400200-18402400	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr19:18400400-18402200	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr19:18400400-18402400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:18400600-18402200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr19:18400600-18402200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:18400600-18402200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:18400600-18402200	Enhancers	Fetal Muscle Leg	muscle
20	chr19:18400600-18402400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:18400600-18402600	Enhancers	Lung	lung
22	chr19:18400600-18404400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:18400800-18402600	Enhancers	NH-A	brain
24	chr19:18400800-18404400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:18401000-18402200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:18401000-18402200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:18401000-18402200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr19:18401000-18402200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr19:18401000-18402200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:18401000-18402200	Enhancers	NHLF	lung
31	chr19:18401000-18402400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr19:18401000-18402400	Enhancers	Placenta Amnion	Placenta Amnion
33	chr19:18401000-18402400	Enhancers	Stomach Mucosa	stomach
34	chr19:18401000-18402600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr19:18401200-18402200	Weak transcription	Ovary	ovary
36	chr19:18401200-18402600	Enhancers	Fetal Heart	heart
37	chr19:18401400-18402200	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr19:18401400-18402200	Weak transcription	HSMM	muscle
39	chr19:18401400-18402400	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr19:18401600-18402200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:18401800-18402200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr19:18401800-18402200	Enhancers	Primary T cells from cord blood	blood
43	chr19:18401800-18402200	Weak transcription	Esophagus	oesophagus
44	chr19:18401800-18402200	Weak transcription	Osteobl	bone
45	chr19:18401800-18402400	Active TSS	Brain Germinal Matrix	brain
46	chr19:18401800-18402600	Enhancers	Fetal Brain Male	brain
47	chr19:18401800-18402600	Enhancers	NHDF-Ad	bronchial
48	chr19:18402000-18402200	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr19:18402000-18402200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr19:18402000-18402200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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