Variant report

Variant	rs6813099
Chromosome Location	chr4:100755107-100755108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:100751084..100753070-chr4:100754307..100755963,2	K562	blood:
2	chr4:100754974..100758082-chr4:100867339..100871318,4	K562	blood:
3	chr4:100742423..100744425-chr4:100753530..100755293,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164031	Chromatin interaction
ENSG00000245322	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1044044	0.90[CEU][hapmap]
rs10516458	0.90[CEU][hapmap];0.88[GIH][hapmap]
rs11097676	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11097678	0.84[EUR][1000 genomes]
rs11097679	0.85[EUR][1000 genomes]
rs11097680	0.89[ASW][hapmap]
rs11097681	0.90[CEU][hapmap];0.88[GIH][hapmap]
rs11723286	0.89[ASW][hapmap];0.82[GIH][hapmap]
rs11736218	0.83[ASW][hapmap];0.90[CEU][hapmap];0.89[GIH][hapmap];0.82[YRI][hapmap]
rs11931053	0.88[ASW][hapmap];0.82[GIH][hapmap]
rs11932783	0.90[CEU][hapmap];0.86[YRI][hapmap]
rs11935458	0.95[CEU][hapmap];0.82[YRI][hapmap];0.88[EUR][1000 genomes]
rs11935615	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs11937985	0.89[ASW][hapmap];0.90[CEU][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap]
rs11939538	0.82[GIH][hapmap]
rs11941799	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs11944405	0.83[ASW][hapmap];0.90[CEU][hapmap];0.88[GIH][hapmap]
rs11944656	0.95[CEU][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs11945303	0.83[ASW][hapmap];0.90[CEU][hapmap];0.89[GIH][hapmap]
rs11947295	0.90[CEU][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs1365491	0.89[ASW][hapmap];0.95[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1465518	0.85[MEX][hapmap]
rs1465519	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17029552	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17029573	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs17029662	0.82[GIH][hapmap]
rs17029673	0.83[ASW][hapmap];0.90[CEU][hapmap];0.88[GIH][hapmap];0.82[YRI][hapmap]
rs2017707	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs2081626	0.90[CEU][hapmap];0.89[GIH][hapmap]
rs2276939	0.90[CEU][hapmap];0.89[GIH][hapmap]
rs34453741	0.85[EUR][1000 genomes]
rs3733463	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3737484	0.89[ASW][hapmap];0.90[CEU][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs3775500	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3775501	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4536938	0.81[AFR][1000 genomes]
rs55973331	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56174126	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57798058	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58304154	0.88[EUR][1000 genomes]
rs58391911	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58534089	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6532834	0.89[ASW][hapmap];0.86[CEU][hapmap];0.88[GIH][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs6814181	0.94[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6816635	0.83[ASW][hapmap];0.82[GIH][hapmap]
rs6817649	0.90[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6829912	0.89[ASW][hapmap];0.90[CEU][hapmap];0.89[GIH][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs6832726	0.90[CEU][hapmap]
rs6848666	0.95[CEU][hapmap];0.96[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs6852487	0.87[CEU][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7666640	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7686565	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7688737	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7697357	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs890486	0.85[EUR][1000 genomes]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6813099	MTTP	cis	lymphoblastoid	seeQTL
rs6813099	DNAJB14	cis	parietal	SCAN
rs6813099	MAPKSP1	cis	cerebellum	SCAN
rs6813099	MAPKSP1	cis	parietal	SCAN
rs6813099	RAP1GDS1	cis	parietal	SCAN
rs6813099	NFKB1	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100740000-100756600	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr4:100741400-100756800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:100741400-100758200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr4:100742800-100756400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:100743600-100756400	Weak transcription	Primary T cells from cord blood	blood
6	chr4:100743600-100758000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr4:100743800-100756800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr4:100744000-100757200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:100744200-100756400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:100744200-100756600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:100744200-100756600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:100744200-100757400	Weak transcription	Spleen	Spleen
13	chr4:100744400-100756600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:100745000-100755800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr4:100745000-100756600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:100745000-100759400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:100745400-100765200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr4:100746200-100756600	Weak transcription	Esophagus	oesophagus
19	chr4:100746400-100759800	Weak transcription	Placenta	Placenta
20	chr4:100747000-100765400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:100749200-100756400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr4:100750200-100756400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr4:100750200-100756600	Weak transcription	GM12878-XiMat	blood
24	chr4:100750800-100759800	Weak transcription	HMEC	breast
25	chr4:100751800-100757400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr4:100752200-100765200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr4:100752400-100755600	Enhancers	Fetal Lung	lung
28	chr4:100753400-100765000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr4:100753600-100755600	Enhancers	Liver	Liver
30	chr4:100753800-100757000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:100753800-100757400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:100754200-100755600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr4:100754200-100761000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr4:100754400-100755200	Enhancers	Colon Smooth Muscle	Colon
35	chr4:100754600-100755200	Enhancers	Ovary	ovary
36	chr4:100754600-100755400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:100754600-100755600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:100754600-100764400	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr4:100754800-100755200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:100754800-100755200	Enhancers	Aorta	Aorta
41	chr4:100754800-100759800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:100755000-100755200	Enhancers	Pancreas	Pancrea
43	chr4:100755000-100755400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr4:100755000-100755400	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr4:100755000-100759800	Strong transcription	NHEK	skin
46	chr4:100755000-100766400	Strong transcription	Primary B cells from cord blood	blood

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