Variant report

Variant	rs4941618
Chromosome Location	chr13:48517289-48517290
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs1104351	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11840968	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11841315	0.82[EUR][1000 genomes]
rs12869161	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874522	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326133	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326137	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327656	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359616	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410116	1.00[CEU][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs1752129	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886977	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927214	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998988	1.00[EUR][1000 genomes]
rs1998989	0.89[EUR][1000 genomes]
rs2025864	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094190	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094193	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094195	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094196	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs2104481	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148939	0.89[EUR][1000 genomes]
rs2148940	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182373	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182375	0.90[MEX][hapmap]
rs2182378	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182785	0.89[EUR][1000 genomes]
rs2406694	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406796	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406798	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765077	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862747	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4427704	0.86[EUR][1000 genomes]
rs4941620	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941624	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942720	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942721	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942723	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4942724	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942732	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942734	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942736	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942740	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942746	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972210	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972223	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972227	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973264	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973265	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973266	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973307	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973308	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974562	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974563	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974564	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974579	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561414	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561416	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561421	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561425	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561426	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561438	0.91[EUR][1000 genomes]
rs7323702	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323821	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324368	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7325175	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326381	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326418	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329137	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329266	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329615	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332363	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332994	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334801	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7335797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336170	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753372	1.00[JPT][hapmap]
rs7985469	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990099	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990541	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991892	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996051	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996581	0.85[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998786	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999270	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs8001032	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8001509	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002322	1.00[MEX][hapmap]
rs8002482	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002847	0.93[EUR][1000 genomes]
rs840428	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840429	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840432	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840435	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840437	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840439	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316340	1.00[ASN][1000 genomes]
rs9316350	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316351	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943066	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943067	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526419	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526431	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526441	0.94[EUR][1000 genomes]
rs9526448	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526455	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs9534884	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534934	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9534956	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534959	0.88[EUR][1000 genomes]
rs9534966	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs9562792	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567927	1.00[JPT][hapmap]
rs9567988	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[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	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS 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	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4941618	MED4	cis	cerebellum	SCAN
rs4941618	MED4	trans	brain	seeQTL
rs4941618	FAM194B	cis	cerebellum	SCAN
rs4941618	MED4	cis	lesional skin	skin_eQTL
rs4941618	MED4	cis	brain	seeQTL
rs4941618	MED4	cis	normal skin	skin_eQTL
rs4941618	MED4	cis	parietal	SCAN
rs4941618	MED4	cis	uninvolved skin	skin_eQTL
rs4941618	SUCLA2	cis	multi-tissue	Pritchard
rs4941618	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs4941618	MED4	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48501000-48531200	Weak transcription	Spleen	Spleen
2	chr13:48502000-48530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:48506000-48531400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr13:48506800-48522600	Weak transcription	Fetal Brain Male	brain
5	chr13:48507200-48524000	Weak transcription	Lung	lung
6	chr13:48507200-48548800	Weak transcription	Stomach Mucosa	stomach
7	chr13:48507800-48530600	Weak transcription	Brain Angular Gyrus	brain
8	chr13:48508000-48522400	Weak transcription	GM12878-XiMat	blood
9	chr13:48508000-48531400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr13:48508200-48520000	Weak transcription	HepG2	liver
11	chr13:48508200-48529600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr13:48508600-48530800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr13:48508800-48522000	Weak transcription	NH-A	brain
14	chr13:48509000-48530800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr13:48509200-48528400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr13:48510800-48517400	Strong transcription	Primary T cells from cord blood	blood
17	chr13:48510800-48517400	Strong transcription	Left Ventricle	heart
18	chr13:48511000-48517600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr13:48511000-48530600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr13:48511000-48536600	Weak transcription	Esophagus	oesophagus
21	chr13:48511800-48518800	Strong transcription	Dnd41	blood
22	chr13:48511800-48531200	Weak transcription	HUVEC	blood vessel
23	chr13:48512000-48517600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr13:48512200-48517600	Strong transcription	Adipose Nuclei	Adipose
25	chr13:48512200-48517600	Strong transcription	Fetal Thymus	thymus
26	chr13:48512200-48522400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr13:48512200-48530000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr13:48512200-48530800	Weak transcription	Colonic Mucosa	Colon
29	chr13:48512200-48531200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr13:48512600-48517600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
31	chr13:48512600-48518600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr13:48512600-48521800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr13:48512600-48522200	Weak transcription	Brain Germinal Matrix	brain
34	chr13:48512600-48527000	Weak transcription	Pancreas	Pancrea
35	chr13:48512600-48529400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr13:48512600-48530800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr13:48512600-48531400	Weak transcription	Aorta	Aorta
38	chr13:48512600-48537600	Weak transcription	Hela-S3	cervix
39	chr13:48512800-48517600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr13:48512800-48518400	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr13:48512800-48522800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr13:48512800-48531200	Weak transcription	Gastric	stomach
43	chr13:48512800-48533800	Weak transcription	NHLF	lung
44	chr13:48513000-48530400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr13:48513000-48531000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr13:48513200-48517400	Strong transcription	Fetal Brain Female	brain
47	chr13:48513200-48518800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr13:48513400-48518000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr13:48513400-48518600	Strong transcription	Placenta	Placenta
50	chr13:48513400-48519000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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