Variant report

Variant	rs2182373
Chromosome Location	chr13:48639352-48639353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48638983..48640532-chr13:48645764..48648632,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1104351	0.96[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	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874522	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326133	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1326137	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1327656	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359616	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410116	0.94[EUR][1000 genomes]
rs1752129	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886977	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927214	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998988	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1998989	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2025864	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094195	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104481	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148939	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2148940	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182378	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182785	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2406694	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406796	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406798	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765077	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862747	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3990876	0.88[AMR][1000 genomes]
rs4427704	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4941618	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941620	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941624	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942720	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942721	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942723	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4942724	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942732	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942734	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942736	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942740	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942746	1.00[AFR][1000 genomes];1.00[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	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973265	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973266	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973307	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973308	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974562	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974563	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974564	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61974579	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561414	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561416	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561421	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561425	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561426	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561438	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7317685	0.96[AMR][1000 genomes]
rs7323702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7323821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7324368	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7325175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326381	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326418	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329615	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332363	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332994	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334801	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7335797	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7336170	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7985469	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990099	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990541	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7991892	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7996581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998786	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999270	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8001032	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8001509	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002482	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002847	0.93[EUR][1000 genomes]
rs840428	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840429	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840432	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840435	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840437	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840439	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316340	1.00[ASN][1000 genomes]
rs9316350	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316351	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943066	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526419	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526431	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526441	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9526448	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526454	0.96[AMR][1000 genomes]
rs9526455	0.96[AMR][1000 genomes]
rs9534884	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534956	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534959	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9534966	0.96[AMR][1000 genomes]
rs9562792	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9567988	0.93[AFR][1000 genomes];1.00[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2182373	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs2182373	MED4	cis	multi-tissue	Pritchard
rs2182373	SUCLA2	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48612600-48640400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:48612600-48645000	Weak transcription	Stomach Mucosa	stomach
3	chr13:48612800-48640200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr13:48612800-48640400	Weak transcription	Psoas Muscle	Psoas
5	chr13:48613000-48640200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr13:48613000-48640400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr13:48613200-48640400	Weak transcription	Fetal Heart	heart
8	chr13:48613200-48641600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr13:48613200-48642200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr13:48613400-48641600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr13:48613400-48647000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr13:48613600-48645000	Weak transcription	Small Intestine	intestine
13	chr13:48616400-48642800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr13:48618800-48644800	Weak transcription	Colonic Mucosa	Colon
15	chr13:48623200-48640200	Weak transcription	Colon Smooth Muscle	Colon
16	chr13:48623200-48652200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr13:48625600-48640200	Weak transcription	Fetal Kidney	kidney
18	chr13:48625600-48640200	Weak transcription	A549	lung
19	chr13:48625800-48640400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr13:48626000-48640200	Weak transcription	HUVEC	blood vessel
21	chr13:48627200-48639400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr13:48627200-48640200	Weak transcription	NH-A	brain
23	chr13:48627200-48640400	Weak transcription	K562	blood
24	chr13:48627400-48639800	Weak transcription	HSMMtube	muscle
25	chr13:48627400-48640200	Weak transcription	Brain Angular Gyrus	brain
26	chr13:48627400-48640200	Weak transcription	Brain Anterior Caudate	brain
27	chr13:48627400-48640200	Weak transcription	Fetal Brain Female	brain
28	chr13:48627400-48640200	Weak transcription	Pancreas	Pancrea
29	chr13:48627400-48640200	Weak transcription	NHDF-Ad	bronchial
30	chr13:48627400-48640400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr13:48627400-48640400	Weak transcription	Lung	lung
32	chr13:48627400-48640800	Weak transcription	Esophagus	oesophagus
33	chr13:48627400-48642200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr13:48627400-48644800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr13:48627400-48645000	Weak transcription	Gastric	stomach
36	chr13:48627400-48645200	Weak transcription	Aorta	Aorta
37	chr13:48627600-48639600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr13:48627600-48640200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr13:48627600-48640200	Weak transcription	Brain Germinal Matrix	brain
40	chr13:48627600-48640200	Weak transcription	Placenta	Placenta
41	chr13:48627600-48640200	Weak transcription	Ovary	ovary
42	chr13:48627600-48640200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr13:48627600-48640200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr13:48627600-48640200	Weak transcription	HepG2	liver
45	chr13:48627600-48640400	Weak transcription	Brain Hippocampus Middle	brain
46	chr13:48627600-48640400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr13:48627600-48640400	Weak transcription	Left Ventricle	heart
48	chr13:48627600-48640600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr13:48627600-48641600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr13:48627600-48642200	Weak transcription	Brain Substantia Nigra	brain

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