Variant report

Variant	rs7990099
Chromosome Location	chr13:48666138-48666139
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48662663..48666159-chr13:48666999..48670435,6	MCF-7	breast:
2	chr13:48653219..48657416-chr13:48663396..48666762,5	K562	blood:

Variant related genes	Relation type
ENSG00000136146	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1104351	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11841315	0.80[EUR][1000 genomes]
rs12869161	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874522	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326133	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326137	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327656	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359616	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410116	1.00[CEU][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs1752129	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886977	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927214	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998988	0.98[EUR][1000 genomes]
rs1998989	0.87[EUR][1000 genomes]
rs2025864	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094190	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094193	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094195	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094196	1.00[JPT][hapmap]
rs2104481	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148939	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2148940	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182373	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182375	1.00[MEX][hapmap]
rs2182378	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182785	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2406694	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406796	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406798	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765077	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862747	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4427704	0.84[EUR][1000 genomes]
rs4941618	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]
rs4941620	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941624	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942720	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942721	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942723	0.90[EUR][1000 genomes]
rs4942724	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942732	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942734	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942736	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942740	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942746	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972223	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61972227	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973264	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973265	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973266	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973307	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973308	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974562	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974563	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974564	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974579	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561414	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561416	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561421	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561425	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561426	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561438	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7317685	0.81[AMR][1000 genomes]
rs7323702	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323821	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324368	0.96[EUR][1000 genomes]
rs7325175	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326381	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326418	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329137	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329266	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329615	1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332363	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332994	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334801	0.88[EUR][1000 genomes]
rs7335797	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]
rs7336170	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985469	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990541	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991892	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]
rs7996051	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996581	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7997347	0.82[MEX][hapmap]
rs7998786	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999270	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8001032	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs8001509	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002322	0.90[MEX][hapmap]
rs8002482	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002847	0.91[EUR][1000 genomes]
rs840428	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840429	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840432	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840435	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840437	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840439	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316340	1.00[ASN][1000 genomes]
rs9316350	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316351	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943066	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943067	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526419	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526431	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526441	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9526448	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526454	0.81[AMR][1000 genomes]
rs9526455	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs9534884	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534934	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9534956	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534959	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9534966	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs9562792	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567988	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[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	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
2	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7990099	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs7990099	MED4	cis	parietal	SCAN
rs7990099	MED4	cis	cerebellum	SCAN
rs7990099	FAM194B	cis	cerebellum	SCAN
rs7990099	MED4	cis	normal skin	skin_eQTL
rs7990099	SUCLA2	cis	multi-tissue	Pritchard
rs7990099	MED4	cis	uninvolved skin	skin_eQTL
rs7990099	MED4	cis	Liver	GTEx
rs7990099	MED4	cis	lesional skin	skin_eQTL
rs7990099	MED4	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48648600-48667400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr13:48652800-48668200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:48653000-48667800	Weak transcription	Stomach Mucosa	stomach
4	chr13:48653000-48668200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:48653200-48668200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr13:48653800-48667600	Weak transcription	A549	lung
7	chr13:48654200-48666800	Weak transcription	Pancreas	Pancrea
8	chr13:48654200-48667600	Weak transcription	Right Ventricle	heart
9	chr13:48655400-48667000	Weak transcription	Gastric	stomach
10	chr13:48655400-48667600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr13:48655400-48668000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr13:48655400-48668200	Weak transcription	Aorta	Aorta
13	chr13:48655600-48666800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr13:48656200-48667000	Weak transcription	HUVEC	blood vessel
15	chr13:48656200-48668000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr13:48657400-48666800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr13:48657400-48666800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr13:48657400-48667600	Weak transcription	Brain Angular Gyrus	brain
19	chr13:48657400-48668000	Weak transcription	HSMMtube	muscle
20	chr13:48657600-48667000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr13:48657600-48667600	Weak transcription	Brain Substantia Nigra	brain
22	chr13:48657800-48667200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr13:48658000-48667000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr13:48658000-48667000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr13:48658000-48667200	Weak transcription	NH-A	brain
26	chr13:48658000-48667600	Weak transcription	Colonic Mucosa	Colon
27	chr13:48658200-48667800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr13:48658400-48666800	Weak transcription	Lung	lung
29	chr13:48658400-48667000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr13:48658600-48666600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr13:48658800-48667600	Weak transcription	Brain Hippocampus Middle	brain
32	chr13:48658800-48667600	Weak transcription	Fetal Brain Male	brain
33	chr13:48658800-48667600	Weak transcription	Fetal Lung	lung
34	chr13:48659000-48667800	Weak transcription	Fetal Kidney	kidney
35	chr13:48659400-48667800	Weak transcription	Brain Germinal Matrix	brain
36	chr13:48659600-48667600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr13:48659600-48668000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr13:48659800-48666800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr13:48659800-48666800	Weak transcription	Primary T cells from cord blood	blood
40	chr13:48659800-48666800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr13:48659800-48666800	Weak transcription	Fetal Intestine Small	intestine
42	chr13:48659800-48667000	Weak transcription	Brain Anterior Caudate	brain
43	chr13:48659800-48667000	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr13:48659800-48667000	Weak transcription	Thymus	Thymus
45	chr13:48659800-48667600	Weak transcription	Fetal Stomach	stomach
46	chr13:48659800-48667600	Weak transcription	Ovary	ovary
47	chr13:48659800-48667800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr13:48659800-48668200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr13:48660000-48666800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr13:48660000-48667400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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