Variant report

Variant	rs202023
Chromosome Location	chr6:13304658-13304659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13282855..13286239-chr6:13300914..13304700,4	K562	blood:
2	chr6:13271941..13273524-chr6:13304499..13306006,2	K562	blood:
3	chr6:13303438..13305943-chr6:13327957..13331432,3	K562	blood:
4	chr6:13304609..13306210-chr6:13327291..13329441,2	K562	blood:
5	chr6:13304377..13307208-chr6:13327707..13329776,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145979	Chromatin interaction
ENSG00000215022	Chromatin interaction
ENSG00000112137	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	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs202016	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202017	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202019	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];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202022	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs202032	0.85[GIH][hapmap]
rs20499	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs20500	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2439534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439535	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439537	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439540	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439542	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439543	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2439544	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2439545	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439549	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458300	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2458309	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2458313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2458314	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2496140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496142	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496144	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496145	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496149	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496151	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496152	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496153	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496154	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496157	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2919685	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2919686	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001966	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001967	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001968	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs364493	1.00[CEU][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3817737	0.80[ASN][1000 genomes]
rs3817738	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs3817741	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs3817742	0.80[ASN][1000 genomes]
rs402705	1.00[CEU][hapmap];0.95[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];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs449727	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]
rs452309	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs453877	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488297	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59639740	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs617580	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs641758	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];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9349564	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9381884	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs9395602	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs957175	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957176	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs202023	TBC1D7	cis	cerebellum	SCAN
rs202023	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13288600-13321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:13288600-13326400	Strong transcription	Primary T cells from cord blood	blood
3	chr6:13289800-13327000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:13290400-13310400	Strong transcription	Dnd41	blood
5	chr6:13291200-13310400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:13291600-13305800	Strong transcription	Thymus	Thymus
7	chr6:13291800-13320400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:13292000-13326000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:13292600-13326600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr6:13293200-13305400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:13295000-13304800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:13295200-13305200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:13298000-13309600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:13298200-13326800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:13299600-13306400	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr6:13299600-13326600	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:13299800-13326400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:13300000-13306400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:13300200-13309200	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr6:13300200-13311800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr6:13300200-13327000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:13301000-13306400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:13301200-13325400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr6:13301800-13307600	Weak transcription	Gastric	stomach
25	chr6:13302200-13305000	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr6:13302200-13305600	Enhancers	Fetal Heart	heart
27	chr6:13302400-13305000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr6:13302400-13305400	Genic enhancers	Fetal Brain Female	brain
29	chr6:13302400-13306400	Enhancers	Primary B cells from peripheral blood	blood
30	chr6:13302600-13304800	Enhancers	Colonic Mucosa	Colon
31	chr6:13302600-13304800	Genic enhancers	Fetal Muscle Leg	muscle
32	chr6:13302600-13304800	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr6:13302600-13304800	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr6:13302600-13305000	Genic enhancers	K562	blood
35	chr6:13302600-13305400	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr6:13302600-13305400	Genic enhancers	Fetal Muscle Trunk	muscle
37	chr6:13302600-13305600	Enhancers	HSMMtube	muscle
38	chr6:13302600-13305800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:13302600-13305800	Strong transcription	Pancreas	Pancrea
40	chr6:13302800-13305600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:13302800-13307200	Weak transcription	Brain Germinal Matrix	brain
42	chr6:13303000-13304800	Enhancers	Primary hematopoietic stem cells	blood
43	chr6:13303200-13304800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:13303200-13305000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr6:13303400-13305400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:13303400-13307600	Genic enhancers	A549	lung
47	chr6:13303400-13309600	Strong transcription	Fetal Thymus	thymus
48	chr6:13303400-13315200	Weak transcription	Small Intestine	intestine
49	chr6:13303400-13315800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr6:13303600-13304800	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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