Variant report

Variant	rs10416055
Chromosome Location	chr19:39435485-39435486
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	chr19:39430639..39433501-chr19:39434198..39436514,3	K562	blood:
2	chr19:39419688..39423695-chr19:39432581..39436696,7	K562	blood:

Variant related genes	Relation type
ENSG00000128626	Chromatin interaction
ENSG00000104835	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10410544	1.00[CHB][hapmap]
rs10425217	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10775533	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11083485	0.81[ASN][1000 genomes]
rs11083489	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11668245	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12462710	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12610409	0.85[ASN][1000 genomes]
rs12972925	0.86[ASN][1000 genomes]
rs12972986	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12979755	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs12982957	0.86[EUR][1000 genomes]
rs17545254	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1808661	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1808662	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1865047	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865049	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2278412	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3136640	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs4801960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap]
rs4801971	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802998	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs4803006	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs4803034	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs575	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7257007	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs730078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7508411	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7508539	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8113389	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9636109	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs9749516	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10416055	LGALS14	cis	parietal	SCAN
rs10416055	MYPOP	cis	parietal	SCAN
rs10416055	GPR4	cis	parietal	SCAN
rs10416055	SARS2	cis	multi-tissue	Pritchard
rs10416055	CTC-360G5.9	cis	Nerve Tibial	GTEx
rs10416055	PRR19	cis	parietal	SCAN
rs10416055	PLD3	cis	parietal	SCAN
rs10416055	SARS2	cis	lymphoblastoid	seeQTL
rs10416055	ZNF285	cis	cerebellum	SCAN
rs10416055	CLPTM1	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39422400-39440600	Weak transcription	NHDF-Ad	bronchial
2	chr19:39422600-39440200	Weak transcription	NH-A	brain
3	chr19:39422600-39440600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr19:39422600-39453000	Weak transcription	HSMMtube	muscle
5	chr19:39423200-39440800	Weak transcription	Fetal Heart	heart
6	chr19:39423400-39436800	Weak transcription	Aorta	Aorta
7	chr19:39423600-39440400	Weak transcription	Right Atrium	heart
8	chr19:39423600-39440600	Weak transcription	Gastric	stomach
9	chr19:39424400-39436800	Weak transcription	Brain Angular Gyrus	brain
10	chr19:39424400-39440000	Weak transcription	Fetal Brain Female	brain
11	chr19:39424600-39436600	Weak transcription	Brain Anterior Caudate	brain
12	chr19:39424600-39440200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr19:39424600-39440200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:39424800-39440200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr19:39424800-39440200	Weak transcription	Brain Substantia Nigra	brain
16	chr19:39425400-39436800	Weak transcription	Lung	lung
17	chr19:39425400-39440400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr19:39425600-39436800	Weak transcription	Brain Hippocampus Middle	brain
19	chr19:39425600-39440200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr19:39425800-39436400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:39425800-39437000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:39425800-39440200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr19:39425800-39440600	Weak transcription	Esophagus	oesophagus
24	chr19:39425800-39440600	Weak transcription	Left Ventricle	heart
25	chr19:39425800-39440600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr19:39425800-39440600	Weak transcription	Right Ventricle	heart
27	chr19:39425800-39440600	Weak transcription	NHEK	skin
28	chr19:39426000-39436600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:39426000-39440200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr19:39426400-39440600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:39431400-39440200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr19:39431400-39440600	Weak transcription	HUVEC	blood vessel
33	chr19:39431600-39439600	Strong transcription	Fetal Muscle Leg	muscle
34	chr19:39431800-39440200	Strong transcription	Fetal Intestine Small	intestine
35	chr19:39432000-39440200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr19:39432200-39440200	Strong transcription	Fetal Stomach	stomach
37	chr19:39432400-39439600	Strong transcription	Fetal Muscle Trunk	muscle
38	chr19:39432400-39441800	Strong transcription	A549	lung
39	chr19:39432600-39440200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr19:39432800-39440200	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr19:39432800-39440800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr19:39433200-39438600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr19:39433200-39439600	Strong transcription	Liver	Liver
44	chr19:39433400-39440600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr19:39433600-39436800	Weak transcription	Spleen	Spleen
46	chr19:39433600-39440200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr19:39433600-39440600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:39433800-39436800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:39433800-39440200	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr19:39434000-39439200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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