Variant report

Variant	rs8104241
Chromosome Location	chr19:36899087-36899088
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12461529	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12462725	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17206379	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385802	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2945955	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2945956	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2945989	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967508	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967511	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967516	0.82[ASN][1000 genomes]
rs2967519	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3098393	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3111555	0.81[ASN][1000 genomes]
rs3111556	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3810326	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56378871	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61706074	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62112567	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62112568	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62112569	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62112624	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62112631	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62112632	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62113869	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7253122	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73043845	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73043902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1066026	chr19:36878441-36947928	ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8104241	LINC00665	cis	Muscle Skeletal	GTEx
rs8104241	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs8104241	LINC00665	cis	Nerve Tibial	GTEx
rs8104241	LINC00665	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36880400-36904600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:36882200-36908800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:36882400-36907600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:36882600-36904200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:36883000-36905200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
6	chr19:36885600-36908000	Weak transcription	K562	blood
7	chr19:36886400-36901000	Weak transcription	Stomach Mucosa	stomach
8	chr19:36888400-36901200	Strong transcription	Brain Hippocampus Middle	brain
9	chr19:36889600-36900200	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr19:36889800-36908200	Weak transcription	HepG2	liver
11	chr19:36890400-36901400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:36891000-36904800	Strong transcription	Dnd41	blood
13	chr19:36891200-36901400	ZNF genes & repeats	A549	lung
14	chr19:36891400-36900200	Strong transcription	Fetal Muscle Leg	muscle
15	chr19:36891800-36908200	Weak transcription	Fetal Heart	heart
16	chr19:36891800-36908200	Weak transcription	Hela-S3	cervix
17	chr19:36892400-36899800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr19:36892400-36901400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:36892400-36901600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr19:36892800-36899400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:36894200-36899400	Strong transcription	Fetal Stomach	stomach
22	chr19:36894400-36899800	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr19:36894400-36900000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:36894400-36900800	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr19:36894400-36901000	Strong transcription	Brain Cingulate Gyrus	brain
26	chr19:36894400-36901200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr19:36894400-36901400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr19:36894400-36901600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr19:36894400-36902600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:36894600-36900400	Strong transcription	Osteobl	bone
31	chr19:36894600-36900800	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr19:36894600-36900800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:36894600-36901000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:36894600-36901200	Strong transcription	NHDF-Ad	bronchial
35	chr19:36894800-36899800	Strong transcription	Fetal Kidney	kidney
36	chr19:36894800-36900600	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr19:36894800-36901000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr19:36894800-36901200	Strong transcription	Colon Smooth Muscle	Colon
39	chr19:36895000-36899400	Strong transcription	Fetal Brain Male	brain
40	chr19:36895000-36900400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:36895000-36900400	Strong transcription	HSMM	muscle
42	chr19:36895000-36900600	Strong transcription	Rectal Smooth Muscle	rectum
43	chr19:36895000-36900800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr19:36895000-36900800	Strong transcription	Brain Anterior Caudate	brain
45	chr19:36895000-36901000	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr19:36895000-36901200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr19:36895000-36901400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr19:36895000-36901400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:36895000-36908200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr19:36895200-36900600	Strong transcription	Skeletal Muscle Female	skeletal muscle

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