Variant report

Variant	rs61972227
Chromosome Location	chr13:48492033-48492034
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1104351	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11840968	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11841315	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12869161	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874522	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326133	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326137	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359616	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410116	0.81[EUR][1000 genomes]
rs1886977	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927214	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2025864	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094190	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094193	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094195	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104481	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148940	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182373	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182378	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406694	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406796	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406798	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862747	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941618	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941620	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941624	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942720	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942721	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942724	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942732	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942734	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942736	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942740	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942746	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972210	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972223	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973264	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973265	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973266	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973307	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973308	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974562	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974563	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974564	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974579	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561414	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561416	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561421	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561425	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561426	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323702	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323821	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324368	0.85[EUR][1000 genomes]
rs7325175	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326418	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329137	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329266	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329615	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332363	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332994	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7335797	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336170	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985469	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990099	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990541	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991892	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996051	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996581	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998786	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8001032	0.87[EUR][1000 genomes]
rs8001509	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002482	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002847	0.89[EUR][1000 genomes]
rs840428	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840429	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840432	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840435	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840437	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840439	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316340	1.00[ASN][1000 genomes]
rs9316350	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316351	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943066	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943067	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526419	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526431	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526441	0.81[EUR][1000 genomes]
rs9534884	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534956	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562792	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567988	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3510679	chr13:48236624-48498185	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3510680	chr13:48236624-48498185	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv3518029	chr13:48491634-48496241	Weak transcription ZNF genes & repeats Active TSS Enhancers	n/a	n/a	inside rSNPs	diseases
6	esv3518040	chr13:48491634-48496241	Weak transcription Enhancers ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs61972227	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs61972227	SUCLA2	cis	multi-tissue	Pritchard
rs61972227	MED4	cis	multi-tissue	Pritchard

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48477000-48506400	Weak transcription	Psoas Muscle	Psoas
2	chr13:48478800-48492200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr13:48481000-48493000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr13:48482800-48494400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:48489400-48492800	Weak transcription	Liver	Liver
6	chr13:48490400-48492200	Enhancers	Dnd41	blood
7	chr13:48490600-48492600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr13:48491000-48492200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr13:48491800-48492200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr13:48491800-48492200	ZNF genes & repeats	Left Ventricle	heart
11	chr13:48492000-48492200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
12	chr13:48492000-48492800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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