Variant report

Variant	rs9321990
Chromosome Location	chr6:145077921-145077922
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	chr6:145071134..145073860-chr6:145076447..145078189,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11969314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219714	0.90[CEU][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1406045	0.89[JPT][hapmap]
rs1590054	0.89[JPT][hapmap]
rs1969517	0.87[AMR][1000 genomes]
rs2328571	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs4131500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243473	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243474	0.83[CHD][hapmap]
rs4272231	0.83[CHD][hapmap]
rs4295503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4305737	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4360150	0.90[CEU][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4446580	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4463276	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4479957	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4538733	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4571589	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4896738	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs4896740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570644	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6901197	0.89[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6906020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906948	0.92[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes]
rs7750326	0.89[ASW][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs7756909	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7758449	0.89[JPT][hapmap]
rs9283116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321988	0.86[AMR][1000 genomes]
rs9373425	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes]
rs9390197	0.89[JPT][hapmap]
rs9390201	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs9390208	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9403587	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1032838	chr6:144978504-145110121	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830833	chr6:145001310-145201143	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1021098	chr6:145017386-145106441	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9321990	PHACTR2	cis	lymphoblastoid	seeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145011800-145090200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr6:145011800-145096600	Weak transcription	Thymus	Thymus
3	chr6:145024000-145087200	Weak transcription	Psoas Muscle	Psoas
4	chr6:145040000-145094600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:145040000-145114600	Weak transcription	NHLF	lung
6	chr6:145046000-145122200	Weak transcription	Colonic Mucosa	Colon
7	chr6:145047600-145083400	Weak transcription	Right Ventricle	heart
8	chr6:145047600-145096600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:145047600-145115000	Weak transcription	Esophagus	oesophagus
10	chr6:145047600-145115000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:145047800-145079600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:145047800-145079600	Weak transcription	NHEK	skin
13	chr6:145049400-145098400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr6:145049600-145088800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:145053000-145079800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:145054000-145095600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr6:145054200-145093400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr6:145054400-145100000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:145056600-145078600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr6:145059600-145096600	Weak transcription	Lung	lung
21	chr6:145059600-145097400	Weak transcription	Spleen	Spleen
22	chr6:145059800-145096600	Weak transcription	Fetal Stomach	stomach
23	chr6:145066200-145090200	Weak transcription	Fetal Kidney	kidney
24	chr6:145066200-145126200	Weak transcription	Stomach Mucosa	stomach
25	chr6:145066400-145087800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr6:145066400-145090400	Weak transcription	Pancreas	Pancrea
27	chr6:145066400-145090600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr6:145067000-145083800	Weak transcription	Fetal Lung	lung
29	chr6:145067800-145078000	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr6:145067800-145115800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr6:145068000-145082200	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr6:145068200-145081000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr6:145068200-145081200	Strong transcription	Dnd41	blood
34	chr6:145068800-145078000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr6:145068800-145080600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:145068800-145090600	Weak transcription	Small Intestine	intestine
37	chr6:145068800-145115000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:145069000-145089200	Weak transcription	HSMMtube	muscle
39	chr6:145069200-145078200	Strong transcription	HepG2	liver
40	chr6:145069400-145078000	Strong transcription	Adipose Nuclei	Adipose
41	chr6:145069400-145080200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:145069400-145080200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:145069600-145093400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:145069800-145094200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:145069800-145101800	Weak transcription	Aorta	Aorta
46	chr6:145070000-145090600	Weak transcription	Left Ventricle	heart
47	chr6:145070000-145092600	Weak transcription	Fetal Intestine Small	intestine
48	chr6:145070200-145088600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr6:145070200-145094000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:145070600-145094400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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