Variant report

Variant	rs1410116
Chromosome Location	chr13:48685916-48685917
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48610309..48612694-chr13:48684921..48687258,2	K562	blood:

Variant related genes	Relation type
ENSG00000136143	Chromatin interaction
ENSG00000136159	Chromatin interaction

Extended variants
information (count: 168 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs1104351	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11148101	0.98[ASN][1000 genomes]
rs11148102	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs11148103	0.98[ASN][1000 genomes]
rs11148104	0.98[ASN][1000 genomes]
rs11148105	0.98[ASN][1000 genomes]
rs11838539	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11840013	0.98[ASN][1000 genomes]
rs11841025	0.89[CHB][hapmap];0.98[ASN][1000 genomes]
rs11841089	0.98[ASN][1000 genomes]
rs11841517	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[MKK][hapmap];0.98[ASN][1000 genomes]
rs11842654	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs12427769	0.98[ASN][1000 genomes]
rs12428098	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs12428738	0.81[ASN][1000 genomes]
rs12428782	0.98[ASN][1000 genomes]
rs12428797	0.98[ASN][1000 genomes]
rs12429895	0.98[ASN][1000 genomes]
rs12429926	0.98[ASN][1000 genomes]
rs12430608	0.82[ASN][1000 genomes]
rs12584124	0.98[ASN][1000 genomes]
rs12584625	0.98[ASN][1000 genomes]
rs12584738	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs12585232	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs12585517	0.98[ASN][1000 genomes]
rs12585766	0.98[ASN][1000 genomes]
rs12869161	0.94[EUR][1000 genomes]
rs12874522	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1326133	0.94[EUR][1000 genomes]
rs1326137	1.00[CEU][hapmap];0.82[TSI][hapmap];0.94[EUR][1000 genomes]
rs1327656	0.94[EUR][1000 genomes]
rs1359616	0.94[EUR][1000 genomes]
rs1752129	0.81[EUR][1000 genomes]
rs1886977	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1927214	0.94[EUR][1000 genomes]
rs1998988	0.94[EUR][1000 genomes]
rs1998989	0.96[EUR][1000 genomes]
rs2025864	0.94[EUR][1000 genomes]
rs2094190	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2094193	0.90[EUR][1000 genomes]
rs2094195	0.89[EUR][1000 genomes]
rs2104481	0.89[EUR][1000 genomes]
rs2148247	0.98[ASN][1000 genomes]
rs2148939	0.96[EUR][1000 genomes]
rs2148940	0.94[EUR][1000 genomes]
rs2182373	0.94[EUR][1000 genomes]
rs2182375	0.82[MEX][hapmap]
rs2182378	0.94[EUR][1000 genomes]
rs2182785	0.96[EUR][1000 genomes]
rs2296572	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs2406694	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2406796	0.94[EUR][1000 genomes]
rs2406798	0.94[EUR][1000 genomes]
rs35535367	0.82[ASN][1000 genomes]
rs3742108	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[MKK][hapmap];0.98[ASN][1000 genomes]
rs3782979	0.90[CHB][hapmap];0.93[CHD][hapmap];0.92[ASN][1000 genomes]
rs3862747	0.94[EUR][1000 genomes]
rs4427704	0.92[EUR][1000 genomes]
rs4941618	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs4941620	0.90[EUR][1000 genomes]
rs4941624	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4942720	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4942721	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4942723	0.86[EUR][1000 genomes]
rs4942724	0.92[EUR][1000 genomes]
rs4942732	0.94[EUR][1000 genomes]
rs4942734	0.94[EUR][1000 genomes]
rs4942736	0.94[EUR][1000 genomes]
rs4942740	0.94[EUR][1000 genomes]
rs4942741	0.84[AMR][1000 genomes]
rs4942746	0.94[EUR][1000 genomes]
rs56670154	0.98[ASN][1000 genomes]
rs58080658	0.98[ASN][1000 genomes]
rs59447207	0.98[ASN][1000 genomes]
rs60828855	0.98[ASN][1000 genomes]
rs61403342	0.98[ASN][1000 genomes]
rs61972227	0.81[EUR][1000 genomes]
rs61973264	0.94[EUR][1000 genomes]
rs61973265	0.94[EUR][1000 genomes]
rs61973266	0.94[EUR][1000 genomes]
rs61973307	0.94[EUR][1000 genomes]
rs61973308	0.90[EUR][1000 genomes]
rs61974562	0.94[EUR][1000 genomes]
rs61974563	0.94[EUR][1000 genomes]
rs61974564	0.94[EUR][1000 genomes]
rs61974579	0.94[EUR][1000 genomes]
rs6561414	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6561416	0.94[EUR][1000 genomes]
rs6561421	0.94[EUR][1000 genomes]
rs6561425	0.94[EUR][1000 genomes]
rs6561426	0.94[EUR][1000 genomes]
rs6561438	0.98[EUR][1000 genomes]
rs7323702	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7323821	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7324368	0.92[EUR][1000 genomes]
rs7325175	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7326381	0.91[EUR][1000 genomes]
rs7326418	0.85[EUR][1000 genomes]
rs7329137	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7329266	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7329615	0.94[EUR][1000 genomes]
rs7332363	1.00[CEU][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs7332994	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7334801	0.84[EUR][1000 genomes]
rs7335797	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7336170	0.94[EUR][1000 genomes]
rs7336631	0.84[AMR][1000 genomes]
rs73477042	0.85[ASN][1000 genomes]
rs73479175	0.98[ASN][1000 genomes]
rs73479183	0.98[ASN][1000 genomes]
rs73479186	0.98[ASN][1000 genomes]
rs73479195	0.98[ASN][1000 genomes]
rs73479199	0.98[ASN][1000 genomes]
rs73479200	0.98[ASN][1000 genomes]
rs73481207	0.98[ASN][1000 genomes]
rs73481212	0.98[ASN][1000 genomes]
rs73481217	0.98[ASN][1000 genomes]
rs73481223	0.98[ASN][1000 genomes]
rs73481228	0.98[ASN][1000 genomes]
rs73481239	0.98[ASN][1000 genomes]
rs73481250	0.98[ASN][1000 genomes]
rs73481261	0.98[ASN][1000 genomes]
rs73481266	0.98[ASN][1000 genomes]
rs73481271	0.98[ASN][1000 genomes]
rs73489207	0.82[ASN][1000 genomes]
rs73489232	0.82[ASN][1000 genomes]
rs73493331	0.82[ASN][1000 genomes]
rs73493345	0.82[ASN][1000 genomes]
rs7982479	0.90[CHB][hapmap]
rs7985469	0.94[EUR][1000 genomes]
rs7990099	1.00[CEU][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs7990408	0.95[ASN][1000 genomes]
rs7990541	0.94[EUR][1000 genomes]
rs7991892	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7996051	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7996581	0.85[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7997347	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs7998786	0.94[EUR][1000 genomes]
rs7999270	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs8001032	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs8001509	0.94[EUR][1000 genomes]
rs8002482	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs8002847	0.87[EUR][1000 genomes]
rs840428	0.94[EUR][1000 genomes]
rs840429	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs840432	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs840435	0.94[EUR][1000 genomes]
rs840437	0.94[EUR][1000 genomes]
rs840439	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9316350	0.94[EUR][1000 genomes]
rs9316351	0.94[EUR][1000 genomes]
rs943066	0.94[EUR][1000 genomes]
rs943067	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9526419	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9526431	0.94[EUR][1000 genomes]
rs9526440	0.84[AMR][1000 genomes]
rs9526441	0.88[EUR][1000 genomes]
rs9526448	0.94[EUR][1000 genomes]
rs9526454	0.85[EUR][1000 genomes]
rs9526455	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes]
rs9534884	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9534934	1.00[CEU][hapmap]
rs9534956	0.94[EUR][1000 genomes]
rs9534959	0.94[EUR][1000 genomes]
rs9534966	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes]
rs9562792	0.94[EUR][1000 genomes]
rs9567988	1.00[CEU][hapmap];0.92[EUR][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	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1410116	MED4	cis	brain	seeQTL
rs1410116	MED4	cis	uninvolved skin	skin_eQTL
rs1410116	MED4	cis	parietal	SCAN
rs1410116	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs1410116	MED4	cis	cerebellum	SCAN
rs1410116	MED4	trans	brain	seeQTL
rs1410116	SCGB1D2	trans	brain	seeQTL
rs1410116	SCGB2A2	trans	brain	seeQTL
rs1410116	FAM194B	cis	cerebellum	SCAN
rs1410116	MED4	cis	lesional skin	skin_eQTL
rs1410116	MED4	cis	normal skin	skin_eQTL
rs1410116	MED4	cis	multi-tissue	Pritchard
rs1410116	SUCLA2	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48683400-48687800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr13:48683600-48686000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr13:48683800-48686400	Enhancers	Brain Anterior Caudate	brain
4	chr13:48683800-48686400	Enhancers	Hela-S3	cervix
5	chr13:48684000-48686600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr13:48684400-48686000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:48684400-48686200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr13:48684600-48686000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:48684600-48686000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr13:48684600-48686000	Enhancers	HMEC	breast
11	chr13:48684600-48686200	Enhancers	Brain Substantia Nigra	brain
12	chr13:48684600-48686400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:48684600-48686400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr13:48684600-48686400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr13:48685000-48686200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr13:48685000-48686400	Enhancers	Small Intestine	intestine
17	chr13:48685000-48688800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:48685000-48689000	Enhancers	Adipose Nuclei	Adipose
19	chr13:48685000-48689200	Enhancers	HepG2	liver
20	chr13:48685200-48686000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr13:48685200-48686200	Enhancers	Brain Angular Gyrus	brain
22	chr13:48685200-48686200	Enhancers	Stomach Smooth Muscle	stomach
23	chr13:48685200-48686400	Enhancers	Brain Cingulate Gyrus	brain
24	chr13:48685200-48686400	Enhancers	Brain Hippocampus Middle	brain
25	chr13:48685200-48686400	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr13:48685200-48687200	Enhancers	Left Ventricle	heart
27	chr13:48685200-48687200	Enhancers	Right Atrium	heart
28	chr13:48685400-48686200	Enhancers	HUVEC	blood vessel
29	chr13:48685600-48686400	Enhancers	Right Ventricle	heart
30	chr13:48685600-48686800	Weak transcription	Placenta	Placenta
31	chr13:48685800-48686800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr13:48685800-48687200	Weak transcription	NH-A	brain
33	chr13:48685800-48687400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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