Variant report

Variant	rs60539437
Chromosome Location	chr6:150129572-150129573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GTF2F1	chr6:150129567-150129579	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:150129036-150129624	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150115210..150117160-chr6:150126668..150131060,3	MCF-7	breast:

Variant related genes	Relation type
PCMT1	TF binding region
ENSG00000219433	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs2343263	1.00[AFR][1000 genomes]
rs41424047	1.00[AFR][1000 genomes]
rs55679019	1.00[AFR][1000 genomes]
rs55734514	1.00[AFR][1000 genomes]
rs55956738	1.00[AFR][1000 genomes]
rs56095145	1.00[AFR][1000 genomes]
rs56196636	0.86[AFR][1000 genomes]
rs56252629	0.86[AFR][1000 genomes]
rs56661428	1.00[AFR][1000 genomes]
rs57679254	1.00[AFR][1000 genomes]
rs58121840	0.86[AFR][1000 genomes]
rs58277211	1.00[AFR][1000 genomes]
rs58319496	0.86[AFR][1000 genomes]
rs58735783	1.00[AFR][1000 genomes]
rs58933940	1.00[AFR][1000 genomes]
rs59528999	1.00[AFR][1000 genomes]
rs59644096	1.00[AFR][1000 genomes]
rs60596573	1.00[AFR][1000 genomes]
rs60619665	1.00[AFR][1000 genomes]
rs60909651	1.00[AFR][1000 genomes]
rs61370787	0.86[AFR][1000 genomes]
rs61528805	1.00[AFR][1000 genomes]
rs61666000	0.86[AFR][1000 genomes]
rs73779509	1.00[AFR][1000 genomes]
rs73779511	1.00[AFR][1000 genomes]
rs73779512	1.00[AFR][1000 genomes]
rs73779515	1.00[AFR][1000 genomes]
rs73779534	1.00[AFR][1000 genomes]
rs73779537	1.00[AFR][1000 genomes]
rs73779540	1.00[AFR][1000 genomes]
rs73779542	1.00[AFR][1000 genomes]
rs73779543	1.00[AFR][1000 genomes]
rs73779545	1.00[AFR][1000 genomes]
rs73779548	1.00[AFR][1000 genomes]
rs73779555	1.00[AFR][1000 genomes]
rs73779556	1.00[AFR][1000 genomes]
rs73779560	1.00[AFR][1000 genomes]
rs73779564	1.00[AFR][1000 genomes]
rs73779567	1.00[AFR][1000 genomes]
rs73779571	1.00[AFR][1000 genomes]
rs73779573	0.86[AFR][1000 genomes]
rs73779577	1.00[AFR][1000 genomes]
rs73781243	1.00[AFR][1000 genomes]
rs73781249	0.86[AFR][1000 genomes]
rs73781250	1.00[AFR][1000 genomes]
rs73781251	1.00[AFR][1000 genomes]
rs73781252	1.00[AFR][1000 genomes]
rs73781278	1.00[AFR][1000 genomes]
rs73781279	1.00[AFR][1000 genomes]
rs73781280	1.00[AFR][1000 genomes]
rs73781281	0.86[AFR][1000 genomes]
rs73781282	1.00[AFR][1000 genomes]
rs73781283	1.00[AFR][1000 genomes]
rs73781284	1.00[AFR][1000 genomes]
rs73781287	1.00[AFR][1000 genomes]
rs73781288	1.00[AFR][1000 genomes]
rs73781290	1.00[AFR][1000 genomes]
rs73782106	0.86[AFR][1000 genomes]
rs73782133	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886762	chr6:149866452-150174507	Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv1803291	chr6:150018508-150164190	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv886763	chr6:150091219-150174507	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	esv1819303	chr6:150093678-150132092	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150072000-150152000	Weak transcription	Aorta	Aorta
2	chr6:150073800-150182400	Weak transcription	Fetal Brain Male	brain
3	chr6:150077400-150142400	Weak transcription	Fetal Heart	heart
4	chr6:150087200-150154000	Weak transcription	Small Intestine	intestine
5	chr6:150087400-150134000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:150088000-150160400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:150093400-150133400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:150093600-150135200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:150094400-150167200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:150098000-150144000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:150105200-150133600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:150105800-150176400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:150112600-150167200	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:150116000-150151800	Weak transcription	NHLF	lung
15	chr6:150118000-150143800	Weak transcription	Hela-S3	cervix
16	chr6:150118800-150151400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:150119000-150131800	Weak transcription	Brain Substantia Nigra	brain
18	chr6:150119000-150132200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:150119000-150132200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:150119000-150140400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:150119000-150144600	Weak transcription	Psoas Muscle	Psoas
22	chr6:150119000-150145600	Weak transcription	Pancreas	Pancrea
23	chr6:150119000-150146600	Weak transcription	Esophagus	oesophagus
24	chr6:150119000-150152600	Weak transcription	A549	lung
25	chr6:150119000-150164000	Weak transcription	Right Ventricle	heart
26	chr6:150119200-150133600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:150119200-150136200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr6:150119200-150142600	Weak transcription	Gastric	stomach
29	chr6:150119400-150142800	Weak transcription	Brain Angular Gyrus	brain
30	chr6:150119400-150146600	Weak transcription	NHEK	skin
31	chr6:150120000-150131000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:150120000-150131200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:150120000-150164600	Weak transcription	Fetal Kidney	kidney
34	chr6:150120400-150144400	Weak transcription	Spleen	Spleen
35	chr6:150120600-150142800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:150121400-150144200	Weak transcription	Fetal Brain Female	brain
37	chr6:150122000-150131000	Weak transcription	HUVEC	blood vessel
38	chr6:150122000-150131200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr6:150122200-150135400	Weak transcription	GM12878-XiMat	blood
40	chr6:150122600-150144600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:150122800-150132600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:150123600-150157000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:150123800-150131800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:150123800-150131800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr6:150123800-150140800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr6:150123800-150155800	Weak transcription	NH-A	brain
47	chr6:150124000-150146600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:150124600-150131400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:150124600-150131600	Weak transcription	NHDF-Ad	bronchial
50	chr6:150124600-150132200	Weak transcription	Brain Germinal Matrix	brain

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