Variant report

Variant	rs4371125
Chromosome Location	chr15:41960304-41960305
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:41951205..41953153-chr15:41959461..41961905,2	MCF-7	breast:
2	chr15:41952550..41954410-chr15:41959320..41962249,3	MCF-7	breast:
3	chr15:41794716..41797159-chr15:41959395..41960897,2	K562	blood:

Variant related genes	Relation type
ENSG00000174197	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10152332	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152364	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775122	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10775123	0.89[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10775124	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1081022	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11070345	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070347	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070350	0.83[EUR][1000 genomes]
rs11632100	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634840	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11639146	0.84[ASN][1000 genomes]
rs11639249	0.84[ASN][1000 genomes]
rs11855017	0.81[ASN][1000 genomes]
rs1197666	0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs1197670	0.83[EUR][1000 genomes]
rs1197704	0.80[CHB][hapmap]
rs1197768	0.90[ASN][1000 genomes]
rs1197769	0.90[ASN][1000 genomes]
rs1197772	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12148330	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441249	0.90[CHB][hapmap];0.82[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900295	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12902548	0.82[ASN][1000 genomes]
rs12915325	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916992	0.89[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648827	0.83[EUR][1000 genomes]
rs1648828	0.83[EUR][1000 genomes]
rs1648829	0.82[EUR][1000 genomes]
rs1648830	0.83[EUR][1000 genomes]
rs1648831	0.83[EUR][1000 genomes]
rs1648832	0.83[EUR][1000 genomes]
rs1648833	0.83[EUR][1000 genomes]
rs1648834	0.83[EUR][1000 genomes]
rs1648835	0.83[EUR][1000 genomes]
rs1672464	0.83[EUR][1000 genomes]
rs1672465	0.83[EUR][1000 genomes]
rs1672466	0.83[EUR][1000 genomes]
rs1867416	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867417	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880937	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1880938	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1899819	0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1899820	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899821	0.80[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918314	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2009310	0.91[ASN][1000 genomes]
rs2141141	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178004	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250964	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577947	0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577950	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577951	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577952	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2577953	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577954	0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577955	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2577958	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2577959	0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2605570	0.90[CHB][hapmap];0.89[ASN][1000 genomes]
rs2695162	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695163	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695164	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2695166	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2695168	0.92[ASN][1000 genomes]
rs2695169	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2918051	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2925337	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2950446	0.89[ASN][1000 genomes]
rs3784282	0.80[EUR][1000 genomes]
rs4078788	0.80[EUR][1000 genomes]
rs4244585	0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4270151	0.92[ASN][1000 genomes]
rs4465584	0.89[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4923908	0.90[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924568	0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924571	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924572	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57498313	0.83[EUR][1000 genomes]
rs62002069	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6493008	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493010	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7164209	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165230	0.83[EUR][1000 genomes]
rs7169496	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169668	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176474	0.89[ASN][1000 genomes]
rs7177911	0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178205	0.90[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027390	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8028886	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8030179	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8034261	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038148	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs8038783	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039440	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs890508	0.83[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	nsv1049514	chr15:41958482-42081210	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4371125	MGA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41954200-41962600	Weak transcription	Spleen	Spleen
2	chr15:41954400-41961600	Weak transcription	Gastric	stomach
3	chr15:41954400-41964600	Weak transcription	Lung	lung
4	chr15:41954400-41970600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:41954400-41978600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:41954400-41982800	Weak transcription	Small Intestine	intestine
7	chr15:41954600-41960400	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr15:41954600-41961000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:41954600-41961000	Weak transcription	Fetal Thymus	thymus
10	chr15:41954600-41961200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:41954600-41961200	Weak transcription	Aorta	Aorta
12	chr15:41954600-41961200	Weak transcription	Fetal Muscle Leg	muscle
13	chr15:41954600-41961400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr15:41954600-41961400	Weak transcription	Ovary	ovary
15	chr15:41954600-41961600	Weak transcription	Esophagus	oesophagus
16	chr15:41954600-41961600	Weak transcription	Placenta	Placenta
17	chr15:41954600-41961600	Weak transcription	Right Atrium	heart
18	chr15:41954600-41961600	Weak transcription	Right Ventricle	heart
19	chr15:41954600-41961800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr15:41954600-41964000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:41954600-41964000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:41954600-41964200	Weak transcription	Fetal Stomach	stomach
23	chr15:41954600-41964800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:41954600-41965600	Weak transcription	Left Ventricle	heart
25	chr15:41954600-41976200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr15:41954600-41983800	Weak transcription	Thymus	Thymus
27	chr15:41954600-42001000	Weak transcription	Colonic Mucosa	Colon
28	chr15:41954800-41961000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:41954800-41961000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr15:41954800-41961000	Weak transcription	Primary T cells from cord blood	blood
31	chr15:41954800-41961200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr15:41954800-41961200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr15:41954800-41961200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr15:41954800-41961200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr15:41954800-41961200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:41954800-41961200	Weak transcription	Adipose Nuclei	Adipose
37	chr15:41954800-41961200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr15:41954800-41961200	Weak transcription	Fetal Intestine Large	intestine
39	chr15:41954800-41961400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr15:41954800-41961600	Weak transcription	Psoas Muscle	Psoas
41	chr15:41954800-41961800	Weak transcription	Liver	Liver
42	chr15:41954800-41963200	Weak transcription	HSMMtube	muscle
43	chr15:41954800-41963800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr15:41954800-41964400	Weak transcription	Brain Angular Gyrus	brain
45	chr15:41954800-41964400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr15:41954800-41964400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr15:41954800-41964600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:41954800-41969000	Weak transcription	Fetal Brain Female	brain
49	chr15:41954800-41976200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr15:41954800-41980800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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