Variant report

Variant	rs2860494
Chromosome Location	chr19:19470426-19470427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19469546..19472054-chr19:19474284..19475951,2	MCF-7	breast:
2	chr19:19469711..19473651-chr19:19475756..19478808,4	K562	blood:
3	chr19:19469138..19472356-chr19:19472972..19475692,3	K562	blood:
4	chr19:19464266..19466426-chr19:19469770..19472098,2	K562	blood:

Variant related genes	Relation type
ENSG00000129933	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10406278	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11555053	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11668203	0.82[EUR][1000 genomes]
rs1557723	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1560687	0.82[EUR][1000 genomes]
rs17216041	0.81[AMR][1000 genomes]
rs17751061	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1989867	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2011503	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2060274	0.82[EUR][1000 genomes]
rs2060275	0.81[EUR][1000 genomes]
rs2315023	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2315282	0.83[EUR][1000 genomes]
rs2905429	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2905433	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2905434	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2916070	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2916072	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2916075	0.82[EUR][1000 genomes]
rs2965178	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2965179	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2965181	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2965184	0.83[EUR][1000 genomes]
rs2965186	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2965190	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2965195	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2965201	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34487417	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4239639	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808944	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4808951	0.81[EUR][1000 genomes]
rs4808962	0.82[EUR][1000 genomes]
rs55765017	0.81[AMR][1000 genomes]
rs55822665	0.81[AMR][1000 genomes]
rs56144632	0.81[AMR][1000 genomes]
rs56212061	0.82[AMR][1000 genomes]
rs56278919	0.81[AMR][1000 genomes]
rs56291054	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57436187	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58074958	0.82[EUR][1000 genomes]
rs6511027	0.81[AMR][1000 genomes]
rs6511029	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72999059	0.81[AMR][1000 genomes]
rs72999063	0.81[AMR][1000 genomes]
rs754256	0.82[EUR][1000 genomes]
rs756997	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs756999	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8100097	0.80[AMR][1000 genomes]
rs8105642	0.82[EUR][1000 genomes]
rs8110171	0.81[EUR][1000 genomes]
rs8110250	0.82[EUR][1000 genomes]
rs8111093	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs998732	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1056419	chr19:19421218-19510611	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2860494	SF4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19433400-19470600	Strong transcription	Fetal Stomach	stomach
2	chr19:19434800-19470600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr19:19435000-19471000	Strong transcription	Fetal Brain Female	brain
4	chr19:19435600-19477600	Weak transcription	Fetal Heart	heart
5	chr19:19440400-19475400	Weak transcription	Right Atrium	heart
6	chr19:19440800-19470600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr19:19446600-19470800	Strong transcription	Fetal Intestine Small	intestine
8	chr19:19454400-19475600	Weak transcription	Fetal Kidney	kidney
9	chr19:19458200-19471800	Weak transcription	Hela-S3	cervix
10	chr19:19458400-19471800	Weak transcription	K562	blood
11	chr19:19459200-19475400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:19460800-19475600	Weak transcription	Psoas Muscle	Psoas
13	chr19:19465200-19483600	Weak transcription	NH-A	brain
14	chr19:19465400-19471800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr19:19466600-19475600	Weak transcription	NHDF-Ad	bronchial
16	chr19:19466800-19475600	Weak transcription	HMEC	breast
17	chr19:19467000-19471800	Weak transcription	Stomach Mucosa	stomach
18	chr19:19467000-19472000	Weak transcription	HepG2	liver
19	chr19:19467200-19471800	Weak transcription	GM12878-XiMat	blood
20	chr19:19467200-19472000	Weak transcription	A549	lung
21	chr19:19467200-19475400	Weak transcription	Small Intestine	intestine
22	chr19:19467200-19475600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr19:19467200-19477600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:19467400-19471600	Weak transcription	Primary B cells from cord blood	blood
25	chr19:19467400-19473000	Weak transcription	HUVEC	blood vessel
26	chr19:19467400-19475400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr19:19467400-19475600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr19:19467400-19475600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr19:19467400-19475600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:19467600-19475600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:19467600-19475600	Weak transcription	HSMM	muscle
32	chr19:19468000-19470600	Strong transcription	Fetal Muscle Trunk	muscle
33	chr19:19468000-19471600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:19468000-19475400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:19468000-19475600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr19:19468200-19471600	Weak transcription	Colon Smooth Muscle	Colon
37	chr19:19468200-19472200	Weak transcription	Ovary	ovary
38	chr19:19468200-19475400	Weak transcription	NHEK	skin
39	chr19:19468200-19477600	Weak transcription	Brain Substantia Nigra	brain
40	chr19:19468400-19470800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:19468400-19471400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr19:19468400-19472800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:19468400-19475400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr19:19468400-19475400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr19:19468400-19475400	Weak transcription	Rectal Smooth Muscle	rectum
46	chr19:19468400-19476000	Weak transcription	Left Ventricle	heart
47	chr19:19468400-19477600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:19468400-19478000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:19468600-19471600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:19468600-19471800	Weak transcription	Primary monocytes fromperipheralblood	blood

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