Variant report

Variant	rs10230343
Chromosome Location	chr7:50512929-50512930
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:50511615..50516146-chr7:50516267..50519150,6	K562	blood:
2	chr7:50509032..50512435-chr7:50512756..50515852,4	K562	blood:
3	chr7:50506044..50507753-chr7:50511426..50513777,3	K562	blood:
4	chr7:50502900..50509783-chr7:50510937..50514726,7	K562	blood:

Variant related genes	Relation type
ENSG00000200815	Chromatin interaction
ENSG00000132436	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10230307	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10232974	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10239496	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10243511	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238133	0.86[CHD][hapmap]
rs11761683	0.86[CHD][hapmap]
rs11768267	0.83[CHD][hapmap]
rs1451373	0.85[JPT][hapmap]
rs1451376	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2060762	0.95[JPT][hapmap]
rs2305358	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3735275	0.95[JPT][hapmap]
rs4947510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4947954	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4947980	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6945253	0.83[ASW][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs7790230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7803247	0.81[CHD][hapmap]
rs896309	0.80[JPT][hapmap]
rs935795	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes];0.98[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10230343	FIGNL1	cis	Nerve Tibial	GTEx
rs10230343	FIGNL1	cis	parietal	SCAN
rs10230343	FIGNL1	cis	cerebellum	SCAN
rs10230343	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs10230343	ZPBP	cis	cerebellum	SCAN
rs10230343	FIGNL1	cis	Adipose Subcutaneous	GTEx
rs10230343	FIGNL1	cis	Thyroid	GTEx
rs10230343	FIGNL1	cis	Esophagus Muscularis	GTEx
rs10230343	FIGNL1	cis	lung	GTEx
rs10230343	IKZF1	cis	lymphoblastoid	seeQTL
rs10230343	FIGNL1	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50486200-50513200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr7:50495200-50513000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr7:50495200-50517200	Weak transcription	Stomach Mucosa	stomach
4	chr7:50495600-50513800	Weak transcription	HepG2	liver
5	chr7:50496000-50513000	Weak transcription	Gastric	stomach
6	chr7:50496200-50517600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr7:50499400-50513000	Weak transcription	Psoas Muscle	Psoas
8	chr7:50500000-50513400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr7:50500600-50513000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:50501000-50517400	Weak transcription	Esophagus	oesophagus
11	chr7:50502200-50513600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:50502400-50517200	Weak transcription	Small Intestine	intestine
13	chr7:50503000-50513000	Weak transcription	Spleen	Spleen
14	chr7:50504200-50513200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr7:50504200-50513800	Weak transcription	NH-A	brain
16	chr7:50504400-50513000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr7:50504400-50513000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr7:50504600-50513000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:50504600-50513000	Weak transcription	Brain Substantia Nigra	brain
20	chr7:50504600-50513000	Strong transcription	Dnd41	blood
21	chr7:50504600-50513200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr7:50504600-50513400	Weak transcription	Brain Angular Gyrus	brain
23	chr7:50504600-50513800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr7:50504600-50515000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr7:50504600-50517200	Weak transcription	Pancreas	Pancrea
26	chr7:50504800-50513000	Weak transcription	Hela-S3	cervix
27	chr7:50504800-50513000	Weak transcription	NHLF	lung
28	chr7:50504800-50513000	Weak transcription	Osteobl	bone
29	chr7:50504800-50513200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr7:50504800-50513200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr7:50504800-50513400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:50504800-50516000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr7:50504800-50516800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr7:50504800-50517400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr7:50505000-50513000	Weak transcription	Left Ventricle	heart
36	chr7:50505000-50513400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr7:50505000-50513800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr7:50505400-50513400	Weak transcription	Colon Smooth Muscle	Colon
39	chr7:50505400-50517200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr7:50505400-50517200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr7:50505600-50515000	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr7:50505600-50515200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr7:50505600-50516600	Weak transcription	Fetal Heart	heart
44	chr7:50505600-50517200	Weak transcription	Colonic Mucosa	Colon
45	chr7:50505800-50515200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:50506000-50515000	Strong transcription	Primary B cells from cord blood	blood
47	chr7:50506200-50513000	Weak transcription	HSMM	muscle
48	chr7:50506200-50513200	Weak transcription	HMEC	breast
49	chr7:50506200-50517200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr7:50506400-50513200	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links