Variant report

Variant	rs10239496
Chromosome Location	chr7:50515557-50515558
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:50513305..50516149-chr7:50518034..50521611,5	MCF-7	breast:
2	chr7:50511615..50516146-chr7:50516267..50519150,6	K562	blood:
3	chr7:50509032..50512435-chr7:50512756..50515852,4	K562	blood:
4	chr7:50508600..50510665-chr7:50513721..50515795,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132436	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10230307	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10230343	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10232974	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10243511	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1451376	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305358	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4947510	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4947954	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4947980	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7790230	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs935795	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes];0.95[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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10239496	FIGNL1	cis	lung	GTEx
rs10239496	FIGNL1	cis	Nerve Tibial	GTEx
rs10239496	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs10239496	FIGNL1	cis	Thyroid	GTEx
rs10239496	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs10239496	FIGNL1	cis	Esophagus Muscularis	GTEx
rs10239496	FIGNL1	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50495200-50517200	Weak transcription	Stomach Mucosa	stomach
2	chr7:50496200-50517600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:50501000-50517400	Weak transcription	Esophagus	oesophagus
4	chr7:50502400-50517200	Weak transcription	Small Intestine	intestine
5	chr7:50504600-50517200	Weak transcription	Pancreas	Pancrea
6	chr7:50504800-50516000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr7:50504800-50516800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:50504800-50517400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr7:50505400-50517200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:50505400-50517200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:50505600-50516600	Weak transcription	Fetal Heart	heart
12	chr7:50505600-50517200	Weak transcription	Colonic Mucosa	Colon
13	chr7:50506200-50517200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:50507000-50516800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:50508800-50517200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:50509400-50517200	Weak transcription	Fetal Intestine Small	intestine
17	chr7:50509400-50517400	Weak transcription	Aorta	Aorta
18	chr7:50511600-50517200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr7:50512000-50517000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr7:50512200-50516800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:50513000-50515600	Strong transcription	Fetal Muscle Trunk	muscle
22	chr7:50513000-50515600	Strong transcription	Fetal Thymus	thymus
23	chr7:50513000-50515800	Strong transcription	Fetal Stomach	stomach
24	chr7:50513000-50516400	Genic enhancers	Dnd41	blood
25	chr7:50513400-50516800	Weak transcription	NHLF	lung
26	chr7:50513600-50517400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr7:50514000-50517200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr7:50514200-50517200	Weak transcription	Fetal Brain Male	brain
29	chr7:50514200-50517200	Enhancers	Hela-S3	cervix
30	chr7:50514400-50516200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr7:50514600-50516600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr7:50514600-50516800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr7:50514600-50516800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr7:50514600-50516800	Weak transcription	Brain Angular Gyrus	brain
35	chr7:50514600-50517000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:50514600-50517200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr7:50514600-50517200	Weak transcription	Psoas Muscle	Psoas
38	chr7:50514600-50517200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr7:50514600-50517200	Weak transcription	Right Ventricle	heart
40	chr7:50514800-50516600	Weak transcription	Brain Germinal Matrix	brain
41	chr7:50514800-50516800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr7:50514800-50516800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr7:50514800-50517000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr7:50514800-50517000	Weak transcription	Fetal Muscle Leg	muscle
45	chr7:50514800-50517400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:50515000-50515800	Weak transcription	HepG2	liver
47	chr7:50515000-50516400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr7:50515000-50516600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:50515000-50516600	Weak transcription	Primary T cells from cord blood	blood
50	chr7:50515000-50516600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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