Variant report

Variant	rs4479957
Chromosome Location	chr6:145071930-145071931
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	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];0.98[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243473	0.96[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];0.87[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];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[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];0.96[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];0.98[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321988	0.86[AMR][1000 genomes]
rs9321990	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]
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
rs4479957	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	chr6:145047200-145077400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:145047600-145075000	Weak transcription	Gastric	stomach
9	chr6:145047600-145083400	Weak transcription	Right Ventricle	heart
10	chr6:145047600-145096600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:145047600-145115000	Weak transcription	Esophagus	oesophagus
12	chr6:145047600-145115000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:145047800-145079600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:145047800-145079600	Weak transcription	NHEK	skin
15	chr6:145049400-145098400	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr6:145049600-145088800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:145051800-145072200	Weak transcription	Osteobl	bone
18	chr6:145053000-145072800	Weak transcription	NHDF-Ad	bronchial
19	chr6:145053000-145079800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:145053200-145073800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:145054000-145072600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:145054000-145095600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr6:145054200-145072600	Weak transcription	HUVEC	blood vessel
24	chr6:145054200-145072800	Weak transcription	Ovary	ovary
25	chr6:145054200-145093400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr6:145054400-145100000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:145056000-145072600	Weak transcription	GM12878-XiMat	blood
28	chr6:145056400-145072600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:145056400-145072800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr6:145056600-145072800	Weak transcription	Fetal Muscle Leg	muscle
31	chr6:145056600-145078600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:145058400-145072000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:145059600-145072000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:145059600-145096600	Weak transcription	Lung	lung
35	chr6:145059600-145097400	Weak transcription	Spleen	Spleen
36	chr6:145059800-145096600	Weak transcription	Fetal Stomach	stomach
37	chr6:145063400-145073600	Weak transcription	Fetal Heart	heart
38	chr6:145066200-145072600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:145066200-145073200	Strong transcription	Primary B cells from cord blood	blood
40	chr6:145066200-145075400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr6:145066200-145077400	Weak transcription	Colon Smooth Muscle	Colon
42	chr6:145066200-145090200	Weak transcription	Fetal Kidney	kidney
43	chr6:145066200-145126200	Weak transcription	Stomach Mucosa	stomach
44	chr6:145066400-145074200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:145066400-145087800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr6:145066400-145090400	Weak transcription	Pancreas	Pancrea
47	chr6:145066400-145090600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr6:145066600-145076800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:145066800-145072400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr6:145066800-145076400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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