Variant report

Variant	rs4394861
Chromosome Location	chr11:72800970-72800971
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10793048	0.85[AFR][1000 genomes]
rs10793054	0.82[YRI][hapmap]
rs10793055	0.86[YRI][hapmap]
rs10793056	0.86[YRI][hapmap]
rs10898885	0.85[AFR][1000 genomes]
rs10898894	0.86[YRI][hapmap]
rs10898895	0.82[YRI][hapmap]
rs11235612	0.86[YRI][hapmap]
rs11822039	0.82[GIH][hapmap];0.82[TSI][hapmap]
rs12294037	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12294533	0.86[YRI][hapmap]
rs12419915	0.92[ASN][1000 genomes]
rs1612659	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1783575	0.87[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2187494	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2276379	0.86[YRI][hapmap]
rs2366256	0.84[AMR][1000 genomes]
rs3862796	0.82[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs4944823	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs593753	0.82[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs6592500	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6592505	0.81[MEX][hapmap]
rs6592508	0.86[YRI][hapmap]
rs6592510	0.87[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7102253	0.89[EUR][1000 genomes]
rs7124723	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7925928	0.82[YRI][hapmap]
rs7936751	0.82[YRI][hapmap]
rs7937701	0.86[YRI][hapmap]
rs7943424	0.80[ASW][hapmap];0.95[YRI][hapmap]
rs9645708	0.86[YRI][hapmap]

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	esv2422418	chr11:72646518-72807865	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv555411	chr11:72647296-72800970	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4394861	FCHSD2	cis	parietal	SCAN
rs4394861	KCNE3	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72746600-72824600	Weak transcription	Thymus	Thymus
2	chr11:72764200-72824600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr11:72773000-72810800	Weak transcription	Fetal Stomach	stomach
4	chr11:72773400-72810400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:72782600-72825200	Weak transcription	Lung	lung
6	chr11:72784400-72806400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr11:72784600-72806400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:72784600-72810800	Weak transcription	Aorta	Aorta
9	chr11:72784600-72812000	Weak transcription	NHEK	skin
10	chr11:72785000-72811000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:72785200-72806600	Weak transcription	Osteobl	bone
12	chr11:72785200-72810600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr11:72786000-72804600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:72786200-72823600	Weak transcription	Placenta	Placenta
15	chr11:72788200-72825400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:72789200-72802200	Weak transcription	Fetal Muscle Leg	muscle
17	chr11:72789200-72806000	Weak transcription	Adipose Nuclei	Adipose
18	chr11:72789200-72806600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr11:72789200-72825000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr11:72789200-72825200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr11:72789400-72806200	Weak transcription	Fetal Heart	heart
22	chr11:72789400-72806400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr11:72789400-72817600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:72789400-72825200	Weak transcription	HSMM	muscle
25	chr11:72789400-72825800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr11:72789600-72803200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:72789600-72806000	Weak transcription	Fetal Lung	lung
28	chr11:72789600-72813400	Weak transcription	Fetal Intestine Large	intestine
29	chr11:72790000-72806400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr11:72790200-72807200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:72791400-72806000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr11:72793200-72810600	Weak transcription	Fetal Intestine Small	intestine
33	chr11:72793200-72824800	Weak transcription	Dnd41	blood
34	chr11:72793600-72850600	Weak transcription	NH-A	brain
35	chr11:72795000-72824800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr11:72795200-72803000	Weak transcription	Fetal Thymus	thymus
37	chr11:72795600-72813600	Weak transcription	Primary T cells from cord blood	blood
38	chr11:72795600-72836000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr11:72795800-72804200	Weak transcription	HUVEC	blood vessel
40	chr11:72795800-72812000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:72796600-72806800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr11:72796800-72803200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr11:72796800-72806200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr11:72797000-72803800	Weak transcription	HSMMtube	muscle
45	chr11:72797000-72804800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr11:72797200-72804200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:72798000-72806000	Weak transcription	Brain Hippocampus Middle	brain
48	chr11:72798200-72809800	Weak transcription	Liver	Liver
49	chr11:72798200-72824600	Weak transcription	HepG2	liver
50	chr11:72799200-72803600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links