Variant report

Variant	rs1529733
Chromosome Location	chr19:39949764-39949765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39948878..39954067-chr19:39954959..39958425,6	K562	blood:
2	chr19:39948861..39951537-chr19:39958018..39962971,5	K562	blood:
3	chr19:39949080..39951026-chr19:39959379..39961536,2	K562	blood:
4	chr19:39937361..39939355-chr19:39949611..39951111,2	K562	blood:
5	chr19:39947880..39949976-chr19:39958655..39960289,2	MCF-7	breast:
6	chr19:39898553..39902206-chr19:39948362..39950815,3	K562	blood:

Variant related genes	Relation type
ENSG00000196235	Chromatin interaction
ENSG00000266559	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10420073	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10423161	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10423921	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10425652	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs10426543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11882744	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1865094	0.82[GIH][hapmap]
rs3786950	0.86[CHB][hapmap]
rs45568533	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4802030	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4802033	0.91[CHB][hapmap];0.88[CHD][hapmap]
rs4803238	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4803241	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4803244	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59269050	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61480418	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62120691	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7245986	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7246329	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73035459	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73035461	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8106642	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	nsv544003	chr19:39937078-39974282	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1529733	B3GNT8	cis	parietal	SCAN
rs1529733	CD177	cis	parietal	SCAN
rs1529733	PRKD2	cis	cerebellum	SCAN
rs1529733	MIA	cis	cerebellum	SCAN
rs1529733	NUMBL	cis	parietal	SCAN
rs1529733	RPS16	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39937000-39971000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39937400-39971000	Weak transcription	Right Atrium	heart
3	chr19:39937600-39950000	Weak transcription	Fetal Brain Male	brain
4	chr19:39938600-39967600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:39939000-39950000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr19:39939000-39953400	Strong transcription	Fetal Intestine Small	intestine
7	chr19:39939200-39967600	Strong transcription	Fetal Thymus	thymus
8	chr19:39939400-39968800	Strong transcription	Fetal Stomach	stomach
9	chr19:39940000-39950400	Weak transcription	Small Intestine	intestine
10	chr19:39940000-39952200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:39940000-39968000	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr19:39940200-39968600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:39940200-39968600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr19:39940200-39968800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:39940200-39970600	Weak transcription	Fetal Heart	heart
16	chr19:39941000-39951800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:39941200-39952800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:39941200-39953200	Strong transcription	Dnd41	blood
19	chr19:39941200-39954200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:39941400-39952200	Strong transcription	Fetal Brain Female	brain
21	chr19:39941400-39967400	Strong transcription	Fetal Intestine Large	intestine
22	chr19:39942000-39967400	Strong transcription	Thymus	Thymus
23	chr19:39942000-39967600	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr19:39942200-39953200	Strong transcription	Brain Angular Gyrus	brain
25	chr19:39942200-39967600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr19:39942200-39967600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:39942200-39967600	Strong transcription	Placenta	Placenta
28	chr19:39942200-39967600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr19:39942200-39967800	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr19:39942400-39952400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr19:39942400-39953400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr19:39942600-39953800	Strong transcription	Ovary	ovary
33	chr19:39942600-39967600	Strong transcription	Liver	Liver
34	chr19:39942800-39967400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:39942800-39967800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr19:39943000-39952200	Strong transcription	GM12878-XiMat	blood
37	chr19:39943000-39952400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:39943000-39967200	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr19:39943000-39967800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr19:39943200-39967800	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr19:39943400-39967400	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr19:39944000-39953600	Strong transcription	Left Ventricle	heart
43	chr19:39944000-39967400	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr19:39944200-39952000	Strong transcription	Skeletal Muscle Male	skeletal muscle
45	chr19:39945200-39952200	Strong transcription	Rectal Smooth Muscle	rectum
46	chr19:39945400-39952200	Strong transcription	Esophagus	oesophagus
47	chr19:39945800-39955400	Weak transcription	Hela-S3	cervix
48	chr19:39945800-39966200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:39946600-39951800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:39946600-39952200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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