Variant report

Variant	rs449727
Chromosome Location	chr6:13296310-13296311
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	chr6:13290208..13292111-chr6:13295404..13298068,2	K562	blood:

Variant related genes	Relation type
ENSG00000272379	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1223397	0.81[JPT][hapmap]
rs13203254	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs202016	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs202017	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs202018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs202019	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs202021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs202022	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs202023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs202032	0.87[GIH][hapmap]
rs20499	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs20500	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2439534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439535	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439540	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439543	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439544	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2439545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439549	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2458300	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2458309	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2458310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2458311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2458312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2458313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2458314	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2496140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2496142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2496144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2496145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2496147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2496148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2496149	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2496151	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2496152	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2496153	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2496154	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2496156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2496157	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2919685	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2919686	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3001966	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3001967	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3001968	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs364493	1.00[CEU][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3817737	0.81[ASN][1000 genomes]
rs3817738	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs3817741	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs3817742	0.81[ASN][1000 genomes]
rs402705	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452309	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs453877	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs488297	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59639740	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs617580	0.88[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs641758	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9349564	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9381884	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs9395602	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs957175	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs957176	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs449727	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL
rs449727	TBC1D7	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
2	chr6:13285400-13302400	Weak transcription	HUVEC	blood vessel
3	chr6:13287000-13303600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:13287800-13298200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:13288200-13296400	Strong transcription	GM12878-XiMat	blood
6	chr6:13288400-13302600	Weak transcription	Hela-S3	cervix
7	chr6:13288400-13302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:13288600-13296400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:13288600-13302400	Strong transcription	Fetal Brain Female	brain
10	chr6:13288600-13302600	Strong transcription	Fetal Muscle Leg	muscle
11	chr6:13288600-13321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:13288600-13326400	Strong transcription	Primary T cells from cord blood	blood
13	chr6:13289000-13299800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:13289800-13327000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:13290200-13302800	Weak transcription	NHEK	skin
16	chr6:13290400-13296800	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr6:13290400-13310400	Strong transcription	Dnd41	blood
18	chr6:13290600-13296800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:13290600-13302800	Weak transcription	Stomach Mucosa	stomach
20	chr6:13290800-13296400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:13291000-13297200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:13291000-13297400	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr6:13291000-13302800	Strong transcription	Fetal Stomach	stomach
24	chr6:13291200-13303000	Strong transcription	Fetal Intestine Small	intestine
25	chr6:13291200-13310400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr6:13291400-13296400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:13291400-13297800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:13291400-13299600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr6:13291400-13300200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:13291400-13303600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr6:13291600-13296400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:13291600-13296400	Strong transcription	Left Ventricle	heart
33	chr6:13291600-13297000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:13291600-13297400	Strong transcription	Gastric	stomach
35	chr6:13291600-13297600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr6:13291600-13298200	Strong transcription	Lung	lung
37	chr6:13291600-13298600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:13291600-13298600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:13291600-13300800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr6:13291600-13302400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:13291600-13302400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr6:13291600-13302600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:13291600-13302600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr6:13291600-13305800	Strong transcription	Thymus	Thymus
45	chr6:13291800-13301800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:13291800-13320400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr6:13292000-13296800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:13292000-13302600	Strong transcription	Fetal Intestine Large	intestine
49	chr6:13292000-13326000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:13292200-13296800	Strong transcription	HepG2	liver

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