Variant report

Variant	rs6485758
Chromosome Location	chr11:47530024-47530025
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47495876..47498563-chr11:47527719..47530859,3	K562	blood:
2	chr11:47524421..47526189-chr11:47528668..47531487,2	K562	blood:
3	chr11:47529126..47530970-chr11:47562135..47565880,3	K562	blood:

Variant related genes	Relation type
ENSG00000149187	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1056387	0.89[JPT][hapmap]
rs10742814	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs10742817	0.84[JPT][hapmap]
rs10769264	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10838702	0.88[CHB][hapmap]
rs10838709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10838725	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838726	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs10838731	0.89[AMR][1000 genomes]
rs10838732	0.95[JPT][hapmap]
rs10838740	0.89[JPT][hapmap]
rs10838746	0.88[JPT][hapmap]
rs11039225	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11039244	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11039266	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs11039280	1.00[JPT][hapmap]
rs11039290	1.00[CEU][hapmap];0.89[AMR][1000 genomes]
rs11039297	0.80[AMR][1000 genomes]
rs11039329	0.89[JPT][hapmap]
rs11039332	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11039345	0.89[JPT][hapmap]
rs12286721	0.89[JPT][hapmap]
rs12292911	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12361415	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs12577643	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12785949	0.88[JPT][hapmap]
rs1377416	0.88[CHB][hapmap]
rs1534576	0.94[CHB][hapmap]
rs2203712	0.95[JPT][hapmap]
rs2242081	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2280231	0.91[CEU][hapmap]
rs2293576	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs3740689	0.83[CHB][hapmap]
rs3740699	0.84[JPT][hapmap]
rs3758655	0.89[JPT][hapmap]
rs4539273	0.89[JPT][hapmap]
rs4752860	0.89[JPT][hapmap]
rs61895112	0.81[EUR][1000 genomes]
rs6485763	0.95[JPT][hapmap]
rs7103648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7104036	0.86[ASN][1000 genomes]
rs7118178	0.86[CEU][hapmap]
rs7120548	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7129797	0.89[JPT][hapmap]
rs71475921	0.89[AMR][1000 genomes]
rs7933019	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7936948	0.89[JPT][hapmap]
rs7939420	0.89[JPT][hapmap]
rs7950696	0.95[JPT][hapmap]
rs874896	0.94[CHB][hapmap]
rs896817	0.88[CHB][hapmap]

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	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6485758	FNBP4	cis	lesional skin	skin_eQTL
rs6485758	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs6485758	C1QTNF4	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47508400-47530200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:47509000-47534400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:47509200-47530400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:47510200-47536800	Weak transcription	Fetal Kidney	kidney
5	chr11:47516800-47530200	Weak transcription	Colonic Mucosa	Colon
6	chr11:47521600-47530200	Weak transcription	Right Ventricle	heart
7	chr11:47521600-47531000	Weak transcription	Lung	lung
8	chr11:47521600-47534000	Weak transcription	Aorta	Aorta
9	chr11:47521600-47534400	Weak transcription	HUVEC	blood vessel
10	chr11:47521800-47531000	Weak transcription	Spleen	Spleen
11	chr11:47522800-47530400	Weak transcription	HepG2	liver
12	chr11:47522800-47536200	Weak transcription	Fetal Brain Female	brain
13	chr11:47523000-47530400	Weak transcription	Esophagus	oesophagus
14	chr11:47523000-47536600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:47523000-47545600	Weak transcription	Dnd41	blood
16	chr11:47523200-47531000	Weak transcription	Right Atrium	heart
17	chr11:47523400-47530400	Weak transcription	Pancreas	Pancrea
18	chr11:47524800-47549600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr11:47526200-47530400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:47526200-47530400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr11:47526200-47531000	Weak transcription	Fetal Muscle Leg	muscle
22	chr11:47526400-47533400	Weak transcription	Fetal Stomach	stomach
23	chr11:47527600-47531600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr11:47527800-47530200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr11:47528000-47530200	Enhancers	Brain Substantia Nigra	brain
26	chr11:47528000-47530200	Enhancers	NHLF	lung
27	chr11:47528000-47530800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr11:47528000-47530800	Genic enhancers	Hela-S3	cervix
29	chr11:47528000-47531200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr11:47528000-47531200	Enhancers	Colon Smooth Muscle	Colon
31	chr11:47528000-47531200	Enhancers	HSMMtube	muscle
32	chr11:47528000-47531400	Enhancers	Primary hematopoietic stem cells	blood
33	chr11:47528000-47531600	Enhancers	Adipose Nuclei	Adipose
34	chr11:47528000-47531800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr11:47528000-47532000	Enhancers	HSMM	muscle
36	chr11:47528000-47532400	Enhancers	Stomach Mucosa	stomach
37	chr11:47528000-47535000	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr11:47528000-47538200	Enhancers	Osteobl	bone
39	chr11:47528200-47530200	Enhancers	Brain Cingulate Gyrus	brain
40	chr11:47528200-47530400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr11:47528200-47530600	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr11:47528200-47530800	Enhancers	K562	blood
43	chr11:47528200-47531000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr11:47528200-47531000	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr11:47528200-47531000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr11:47528200-47531200	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr11:47528200-47531200	Enhancers	Primary B cells from cord blood	blood
48	chr11:47528200-47531200	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr11:47528200-47531800	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr11:47528200-47531800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links