Variant report

Variant	rs6561414
Chromosome Location	chr13:48506883-48506884
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1104351	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11840968	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11841315	0.86[EUR][1000 genomes]
rs12869161	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874522	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326133	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326137	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327656	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359616	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410116	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1886977	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927214	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998988	0.95[EUR][1000 genomes]
rs1998989	0.85[EUR][1000 genomes]
rs2025864	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094190	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094193	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094195	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094196	1.00[JPT][hapmap]
rs2104481	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148940	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182373	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182378	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182785	0.85[EUR][1000 genomes]
rs2406694	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406796	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406798	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862747	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4427704	0.82[EUR][1000 genomes]
rs4941618	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941620	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941624	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942720	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942721	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942723	0.87[EUR][1000 genomes]
rs4942724	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942732	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942734	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942736	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942740	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942746	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972210	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972223	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972227	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973264	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973265	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973266	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973307	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973308	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974562	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974563	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974564	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974579	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561416	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561421	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561425	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561426	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561438	0.87[EUR][1000 genomes]
rs7323702	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323821	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324368	0.93[EUR][1000 genomes]
rs7325175	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326381	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326418	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329137	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329266	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329615	1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332363	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332994	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334801	0.86[EUR][1000 genomes]
rs7335797	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336170	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753372	1.00[JPT][hapmap]
rs7985469	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990099	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990541	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991892	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996051	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996581	0.85[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998786	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999270	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs8001032	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes]
rs8001509	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002482	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002847	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs840428	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840429	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840432	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840435	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840437	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840439	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316340	1.00[ASN][1000 genomes]
rs9316350	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316351	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943066	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943067	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526419	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526431	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526441	0.89[EUR][1000 genomes]
rs9526448	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534884	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534934	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9534956	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534959	0.83[EUR][1000 genomes]
rs9562792	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567927	1.00[JPT][hapmap]
rs9567988	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv1803690	chr13:48470681-48508091	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6561414	MED4	cis	normal skin	skin_eQTL
rs6561414	MED4	cis	multi-tissue	Pritchard
rs6561414	MED4	cis	uninvolved skin	skin_eQTL
rs6561414	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs6561414	MED4	cis	lesional skin	skin_eQTL
rs6561414	SUCLA2	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48492200-48510800	Weak transcription	Left Ventricle	heart
2	chr13:48501000-48531200	Weak transcription	Spleen	Spleen
3	chr13:48502000-48530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:48502600-48507000	Weak transcription	Adipose Nuclei	Adipose
5	chr13:48502600-48513600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr13:48503600-48512400	Weak transcription	Aorta	Aorta
7	chr13:48503800-48507000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:48503800-48507400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr13:48503800-48513200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr13:48503800-48516800	Weak transcription	NHDF-Ad	bronchial
11	chr13:48504000-48513400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr13:48506000-48531400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr13:48506400-48508200	Enhancers	Psoas Muscle	Psoas
14	chr13:48506400-48508800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr13:48506400-48508800	Enhancers	H9 Cell Line	embryonic stem cell
16	chr13:48506400-48509000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr13:48506400-48509200	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr13:48506400-48509400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr13:48506600-48507200	Enhancers	HepG2	liver
20	chr13:48506600-48507600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr13:48506600-48508800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr13:48506800-48507000	Enhancers	Brain Anterior Caudate	brain
23	chr13:48506800-48507000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr13:48506800-48507000	Enhancers	Stomach Mucosa	stomach
25	chr13:48506800-48507800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr13:48506800-48508200	Enhancers	Fetal Muscle Leg	muscle
27	chr13:48506800-48508400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr13:48506800-48508800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr13:48506800-48508800	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr13:48506800-48509200	Enhancers	HSMMtube	muscle
31	chr13:48506800-48509400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr13:48506800-48509600	Enhancers	HSMM	muscle
33	chr13:48506800-48522600	Weak transcription	Fetal Brain Male	brain

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