Variant report

Variant	rs11931053
Chromosome Location	chr4:100823058-100823059
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:100810623..100827791-chr4:100865444..100874425,55	K562	blood:
2	chr4:100822597..100824617-chr4:100866275..100869392,5	K562	blood:
3	chr4:100820568..100823308-chr4:100824900..100827243,2	K562	blood:
4	chr4:100815631..100818960-chr4:100821744..100826195,4	K562	blood:

Variant related genes	Relation type
ENSG00000164032	Chromatin interaction
ENSG00000245322	Chromatin interaction
ENSG00000109270	Chromatin interaction
ENSG00000164031	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1044044	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516458	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097676	0.88[ASW][hapmap]
rs11097679	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097680	1.00[ASW][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097681	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097682	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097683	0.98[ASN][1000 genomes]
rs11097685	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11097686	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11723286	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11736218	0.94[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11736750	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11931551	0.95[ASN][1000 genomes]
rs11932783	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11935458	0.81[CHB][hapmap];0.92[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11935615	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11936309	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11936580	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11937985	1.00[ASW][hapmap];0.82[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11938952	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11939538	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11941799	0.94[ASW][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11942532	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs11944405	0.94[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11944656	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11945303	0.94[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11947295	0.82[CEU][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11947412	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1465518	0.92[JPT][hapmap]
rs1465519	0.91[JPT][hapmap]
rs17029573	0.89[ASW][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17029662	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17029673	0.94[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17029724	0.89[ASN][1000 genomes]
rs2017707	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2070738	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2081626	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081627	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162386	0.92[JPT][hapmap]
rs2276939	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2866179	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34453741	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3733463	0.88[ASW][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap]
rs3737484	1.00[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775500	0.88[ASW][hapmap]
rs3775501	0.88[ASW][hapmap]
rs3775512	0.84[JPT][hapmap]
rs3822103	0.92[JPT][hapmap]
rs4320141	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4536938	0.87[ASN][1000 genomes]
rs5015717	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55726736	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55797991	0.86[ASN][1000 genomes]
rs55888547	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56007968	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56140620	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57322716	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58304154	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs60070547	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61191235	0.81[ASN][1000 genomes]
rs61203457	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62305038	0.87[ASN][1000 genomes]
rs62306101	0.92[ASN][1000 genomes]
rs6532834	1.00[ASW][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6532837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6532839	0.89[ASN][1000 genomes]
rs6532840	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6813099	0.88[ASW][hapmap];0.82[GIH][hapmap]
rs6814140	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6814181	0.94[ASW][hapmap];0.86[JPT][hapmap]
rs6816635	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6824513	0.92[ASN][1000 genomes]
rs6829912	1.00[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6831193	0.95[ASN][1000 genomes]
rs6832726	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838495	0.94[ASN][1000 genomes]
rs6842840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6843247	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6845556	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6848666	0.81[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72686215	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs732386	0.94[ASN][1000 genomes]
rs73832925	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7660185	0.92[ASN][1000 genomes]
rs7666156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7666192	0.80[ASN][1000 genomes]
rs7686565	0.92[JPT][hapmap]
rs7687287	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs890486	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[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	nsv879661	chr4:100805207-100869635	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv980462	chr4:100819647-100825036	Strong transcription Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11931053	MAPKSP1	cis	cerebellum	SCAN
rs11931053	MAPKSP1	cis	parietal	SCAN
rs11931053	MTTP	cis	lymphoblastoid	seeQTL
rs11931053	DNAJB14	cis	parietal	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100815600-100840000	Weak transcription	Small Intestine	intestine
2	chr4:100816000-100823200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:100816000-100829600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:100816000-100839800	Weak transcription	Esophagus	oesophagus
5	chr4:100816000-100867000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:100816000-100867000	Weak transcription	Lung	lung
7	chr4:100816200-100823200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:100816200-100823200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:100816200-100823200	Weak transcription	Ovary	ovary
10	chr4:100816200-100823400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:100816200-100823400	Weak transcription	Brain Anterior Caudate	brain
12	chr4:100816200-100823400	Weak transcription	HSMMtube	muscle
13	chr4:100816200-100823600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr4:100816200-100823800	Weak transcription	Brain Angular Gyrus	brain
15	chr4:100816200-100827000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:100816200-100827200	Weak transcription	Brain Hippocampus Middle	brain
17	chr4:100816200-100827400	Weak transcription	K562	blood
18	chr4:100816200-100837600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr4:100816200-100838000	Weak transcription	Fetal Stomach	stomach
20	chr4:100816200-100838800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr4:100816200-100839800	Weak transcription	Aorta	Aorta
22	chr4:100816200-100840200	Weak transcription	Colonic Mucosa	Colon
23	chr4:100816200-100842200	Weak transcription	Pancreas	Pancrea
24	chr4:100816200-100851400	Weak transcription	A549	lung
25	chr4:100816200-100851600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:100816200-100853600	Weak transcription	NHLF	lung
27	chr4:100816200-100866200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr4:100816400-100823200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:100816400-100823200	Weak transcription	Primary T cells from cord blood	blood
30	chr4:100816400-100823200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr4:100816400-100823400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr4:100816400-100823400	Weak transcription	Fetal Muscle Leg	muscle
33	chr4:100816400-100823400	Weak transcription	Psoas Muscle	Psoas
34	chr4:100816400-100824000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr4:100816400-100824600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr4:100816400-100827000	Weak transcription	Fetal Brain Male	brain
37	chr4:100816400-100827000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr4:100816400-100827200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr4:100816400-100828600	Weak transcription	HepG2	liver
40	chr4:100816400-100830600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr4:100816400-100837400	Weak transcription	Thymus	Thymus
42	chr4:100816400-100845800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr4:100816600-100823200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:100816600-100823200	Weak transcription	Left Ventricle	heart
45	chr4:100816600-100823600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr4:100816600-100823800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:100816600-100823800	Weak transcription	Brain Substantia Nigra	brain
48	chr4:100816600-100824400	Weak transcription	Fetal Brain Female	brain
49	chr4:100816600-100827000	Weak transcription	Brain Germinal Matrix	brain
50	chr4:100816600-100827200	Weak transcription	Colon Smooth Muscle	Colon

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