Variant report

Variant	rs11945303
Chromosome Location	chr4:100810611-100810612
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	chr4:100802165..100805574-chr4:100807922..100811974,3	K562	blood:
2	chr4:100799869..100822436-chr4:100866015..100873106,54	K562	blood:

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

Extended variants
information (count: 98 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1044044	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10516458	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097676	0.83[ASW][hapmap];0.85[CEU][hapmap]
rs11097679	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097680	0.94[ASW][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097681	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097682	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097683	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11097685	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11097686	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11723286	0.94[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736218	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11736750	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11931053	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]
rs11931551	0.92[ASN][1000 genomes]
rs11932783	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11935458	0.95[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11935615	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11936309	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11936580	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11937985	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11938952	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11939538	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11941520	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11941799	0.88[ASW][hapmap];0.95[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11942532	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs11944405	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11944656	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11947295	0.90[CEU][hapmap];0.96[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11947412	0.81[JPT][hapmap]
rs1365491	0.85[CEU][hapmap]
rs1465518	0.92[JPT][hapmap]
rs1465519	0.89[CEU][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs17029573	0.94[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17029662	0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17029673	0.88[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17029724	0.91[ASN][1000 genomes]
rs2017707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2070738	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2081626	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2081627	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2162386	0.92[JPT][hapmap]
rs2276939	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2866179	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34453741	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733463	0.83[ASW][hapmap];0.90[CEU][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.81[EUR][1000 genomes]
rs3737484	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775500	0.83[ASW][hapmap];0.85[CEU][hapmap]
rs3775501	0.83[ASW][hapmap];0.85[CEU][hapmap]
rs3775512	0.84[JPT][hapmap]
rs3822103	0.92[JPT][hapmap]
rs4320141	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4536938	0.91[ASN][1000 genomes]
rs5015717	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs55726736	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55797991	0.89[ASN][1000 genomes]
rs55888547	0.91[ASN][1000 genomes]
rs56007968	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56140620	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57322716	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57798058	0.80[EUR][1000 genomes]
rs58304154	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58391911	0.82[EUR][1000 genomes]
rs58534089	0.80[EUR][1000 genomes]
rs60070547	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61191235	0.82[ASN][1000 genomes]
rs61203457	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62305038	0.91[ASN][1000 genomes]
rs62306101	0.93[ASN][1000 genomes]
rs6532834	0.94[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532837	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6532839	0.91[ASN][1000 genomes]
rs6532840	0.91[ASN][1000 genomes]
rs6813099	0.83[ASW][hapmap];0.90[CEU][hapmap];0.89[GIH][hapmap]
rs6814140	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6814181	0.89[ASW][hapmap];0.90[CEU][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs6816635	0.88[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6817649	0.90[CEU][hapmap];0.85[GIH][hapmap]
rs6824513	0.93[ASN][1000 genomes]
rs6829912	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6831193	0.92[ASN][1000 genomes]
rs6832726	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6838495	0.91[ASN][1000 genomes]
rs6842840	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6843247	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6845556	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6848666	0.95[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72686215	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs732386	0.91[ASN][1000 genomes]
rs73832925	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7660185	0.93[ASN][1000 genomes]
rs7666156	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7666640	0.80[EUR][1000 genomes]
rs7686565	0.90[CEU][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs7687287	0.81[CEU][hapmap];0.84[JPT][hapmap]
rs7688737	0.81[EUR][1000 genomes]
rs890486	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11945303	NFKB1	cis	cerebellum	SCAN
rs11945303	MTTP	cis	lymphoblastoid	seeQTL
rs11945303	MAPKSP1	cis	parietal	SCAN
rs11945303	MAPKSP1	cis	cerebellum	SCAN
rs11945303	DNAJB14	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100789600-100814200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr4:100790400-100814600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:100798000-100810800	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr4:100798400-100814200	Weak transcription	Stomach Mucosa	stomach
5	chr4:100799000-100813400	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr4:100799200-100811000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr4:100799400-100812200	Weak transcription	HepG2	liver
8	chr4:100799600-100814800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:100800200-100814200	Weak transcription	Hela-S3	cervix
10	chr4:100801800-100814400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr4:100801800-100814600	Weak transcription	Psoas Muscle	Psoas
12	chr4:100802000-100812200	Weak transcription	Brain Angular Gyrus	brain
13	chr4:100802000-100814200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:100802000-100814200	Weak transcription	Aorta	Aorta
15	chr4:100802000-100814200	Weak transcription	Brain Germinal Matrix	brain
16	chr4:100802000-100814200	Weak transcription	Spleen	Spleen
17	chr4:100802000-100814200	Weak transcription	NHLF	lung
18	chr4:100802000-100814400	Weak transcription	Pancreas	Pancrea
19	chr4:100802200-100812800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:100802200-100814000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:100802200-100814200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:100802200-100814200	Weak transcription	Colonic Mucosa	Colon
23	chr4:100802200-100814200	Weak transcription	A549	lung
24	chr4:100802200-100814600	Weak transcription	Fetal Stomach	stomach
25	chr4:100802200-100814800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:100802200-100814800	Weak transcription	Esophagus	oesophagus
27	chr4:100802200-100814800	Weak transcription	Lung	lung
28	chr4:100802400-100813600	Weak transcription	Small Intestine	intestine
29	chr4:100802400-100814000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:100802400-100814200	Weak transcription	Ovary	ovary
31	chr4:100802400-100814200	Weak transcription	Right Ventricle	heart
32	chr4:100802400-100814200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:100802400-100814200	Weak transcription	Thymus	Thymus
34	chr4:100802400-100814400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr4:100802800-100812400	Weak transcription	Fetal Brain Female	brain
36	chr4:100803000-100814200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr4:100803000-100814200	Weak transcription	Fetal Brain Male	brain
38	chr4:100803000-100814200	Weak transcription	HSMMtube	muscle
39	chr4:100803200-100812400	Weak transcription	Primary T cells from cord blood	blood
40	chr4:100803200-100812400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr4:100803200-100814000	Weak transcription	Brain Substantia Nigra	brain
42	chr4:100803200-100814400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr4:100803400-100812400	Weak transcription	K562	blood
44	chr4:100803400-100813400	Weak transcription	Fetal Heart	heart
45	chr4:100803400-100813600	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr4:100803600-100812200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr4:100803600-100814200	Weak transcription	Brain Hippocampus Middle	brain
48	chr4:100804400-100814400	Weak transcription	Fetal Kidney	kidney
49	chr4:100805200-100814400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:100805400-100812600	Weak transcription	Brain Anterior Caudate	brain

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