Variant report

Variant	rs1968359
Chromosome Location	chr19:40890938-40890939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40889409..40892368-chr19:40893156..40896044,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLD3-2	chr19:40890708-40890998	NONHSAT066379

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11668006	1.00[CHD][hapmap]
rs12978012	0.80[ASN][1000 genomes]
rs3760636	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4803329	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803331	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803334	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6508937	1.00[CHD][hapmap]
rs6508938	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv911707	chr19:40855255-40948202	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv911708	chr19:40855255-40982375	Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
7	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1968359	MEIS3	cis	parietal	SCAN
rs1968359	C5AR1	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40872800-40904400	Weak transcription	Right Atrium	heart
2	chr19:40879000-40898600	Weak transcription	NHEK	skin
3	chr19:40884800-40891000	Weak transcription	A549	lung
4	chr19:40885000-40904400	Weak transcription	Fetal Lung	lung
5	chr19:40885000-40909200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:40885000-40909200	Weak transcription	Aorta	Aorta
7	chr19:40885200-40892800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr19:40885200-40893600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr19:40885200-40904200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:40885400-40894200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:40885400-40909600	Weak transcription	Pancreas	Pancrea
12	chr19:40885600-40898000	Weak transcription	Esophagus	oesophagus
13	chr19:40885800-40893800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr19:40886600-40894800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:40886800-40893800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr19:40886800-40904200	Weak transcription	Right Ventricle	heart
17	chr19:40886800-40909200	Weak transcription	Colon Smooth Muscle	Colon
18	chr19:40887000-40896400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr19:40887000-40898200	Weak transcription	Gastric	stomach
20	chr19:40887000-40898200	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr19:40887000-40909000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:40887200-40893000	Weak transcription	Fetal Muscle Leg	muscle
23	chr19:40887200-40898000	Weak transcription	Lung	lung
24	chr19:40887200-40898600	Weak transcription	Spleen	Spleen
25	chr19:40887400-40893800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr19:40887400-40898800	Weak transcription	Ovary	ovary
27	chr19:40887400-40901600	Weak transcription	Fetal Intestine Small	intestine
28	chr19:40887400-40909000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr19:40887600-40900600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:40887800-40901200	Weak transcription	Fetal Stomach	stomach
31	chr19:40887800-40909200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr19:40890000-40895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:40890000-40895600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:40890000-40904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:40890200-40892200	Weak transcription	Placenta	Placenta
36	chr19:40890200-40895400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:40890200-40895400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr19:40890200-40898800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr19:40890800-40891000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr19:40890800-40891000	Enhancers	Fetal Heart	heart
41	chr19:40890800-40891200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr19:40890800-40891200	Enhancers	HepG2	liver
43	chr19:40890800-40891200	Enhancers	HSMMtube	muscle
44	chr19:40890800-40891400	Enhancers	K562	blood

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