Variant report

Variant	rs72832596
Chromosome Location	chr6:25962951-25962952
allele	A/C
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	MAX	chr6:25962479-25963310	Hela-S3	cervix:	n/a	chr6:25962830-25962839
2	TBL1XR1	chr6:25962371-25963441	GM12878	blood:	n/a	n/a
3	EBF1	chr6:25962350-25963217	GM12878	blood:	n/a	chr6:25962733-25962742 chr6:25962731-25962742 chr6:25962731-25962744 chr6:25962733-25962742 chr6:25962733-25962743
4	FOS	chr6:25962492-25963084	MCF10A-Er-Src	breast:	n/a	chr6:25962588-25962598 chr6:25962588-25962598 chr6:25962985-25962994 chr6:25962588-25962598 chr6:25962588-25962598
5	BCLAF1	chr6:25962426-25963303	GM12878	blood:	n/a	chr6:25963002-25963011
6	ELF1	chr6:25962657-25963211	HepG2	liver:	n/a	n/a
7	KAP1	chr6:25962538-25963196	U2OS	brain:	n/a	n/a
8	POLR2A	chr6:25962340-25963662	GM15510	blood:	n/a	n/a
9	POLR2A	chr6:25962573-25963437	HUVEC	blood vessel:	n/a	n/a
10	EP300	chr6:25962454-25963333	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:25962586-25963427	U87	brain:	n/a	n/a
12	CHD1	chr6:25962426-25963443	GM12878	blood:	n/a	n/a
13	ELK1	chr6:25962500-25963263	GM12878	blood:	n/a	n/a
14	HCFC1	chr6:25962546-25963224	K562	blood:	n/a	n/a
15	POLR2A	chr6:25962503-25963448	U87	brain:	n/a	n/a
16	POLR2A	chr6:25962532-25963290	U87	brain:	n/a	n/a
17	BRCA1	chr6:25962579-25963275	Hela-S3	cervix:	n/a	n/a
18	RELA	chr6:25962497-25963296	GM15510	blood:	n/a	n/a
19	TAF1	chr6:25962901-25963276	K562	blood:	n/a	n/a
20	RUNX3	chr6:25962409-25963258	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:25962596-25964115	IMR90	lung:	n/a	n/a
22	NFIC	chr6:25962716-25963262	HepG2	liver:	n/a	n/a
23	ELF1	chr6:25962586-25963291	HepG2	liver:	n/a	n/a
24	ZMIZ1	chr6:25962740-25963383	K562	blood:	n/a	n/a
25	POLR2A	chr6:25962554-25963221	HCT-116	colon:	n/a	n/a
26	POLR2A	chr6:25962764-25963441	HepG2	liver:	n/a	n/a
27	ELF1	chr6:25962741-25963309	GM12878	blood:	n/a	n/a
28	CCNT2	chr6:25962897-25963307	K562	blood:	n/a	chr6:25963168-25963177
29	POLR2A	chr6:25962865-25963324	Gliobla	brain:	n/a	n/a
30	NFYB	chr6:25962550-25963155	Hela-S3	cervix:	n/a	chr6:25962853-25962868
31	POLR2A	chr6:25962886-25963202	MCF-7	breast:	n/a	n/a
32	UBTF	chr6:25962765-25963917	K562	blood:	n/a	n/a
33	RCOR1	chr6:25962582-25963141	K562	blood:	n/a	n/a
34	POLR2A	chr6:25962706-25963337	K562	blood:	n/a	n/a
35	USF1	chr6:25962555-25963007	A549	lung:	n/a	chr6:25962828-25962839
36	BCL11A	chr6:25962872-25963163	GM12878	blood:	n/a	chr6:25963002-25963011
37	TAF1	chr6:25962837-25963309	GM12892	blood:	n/a	n/a
38	MTA3	chr6:25962288-25963326	GM12878	blood:	n/a	n/a
39	STAT2	chr6:25962759-25963266	K562	blood:	n/a	chr6:25962997-25963012 chr6:25963000-25963011
40	PML	chr6:25962879-25963242	GM12878	blood:	n/a	n/a
41	TAL1	chr6:25962907-25963966	K562	blood:	n/a	n/a
42	FOXM1	chr6:25962438-25963424	GM12878	blood:	n/a	n/a
43	POU2F2	chr6:25962871-25963369	GM12891	blood:	n/a	n/a
44	POLR2A	chr6:25962808-25963419	GM12891	blood:	n/a	n/a
45	SPI1	chr6:25962293-25963534	GM12878	blood:	n/a	chr6:25962799-25962812
46	ELF1	chr6:25962696-25963250	MCF-7	breast:	n/a	n/a
47	TAF1	chr6:25962907-25963181	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr6:25962283-25964437	GM12892	blood:	n/a	n/a
49	ELF1	chr6:25962593-25963344	K562	blood:	n/a	n/a
50	TAF1	chr6:25962872-25963249	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:220024854..220025531-chr6:25962587..25963447,2	Hela-S3	cervix:
2	chr1:68150800..68151500-chr6:25962668..25963223,2	Hela-S3	cervix:
3	chr6:25962020..25964518-chr6:25991024..25993046,2	MCF-7	breast:
4	chr1:37939794..37940755-chr6:25962720..25963450,2	Hela-S3	cervix:
5	chr6:25962825..25963375-chr6:25992746..25993257,2	K562	blood:
6	chr6:25961783..25964529-chr6:25992813..25995946,4	MCF-7	breast:

Variant related genes	Relation type
TRIM38	TF binding region
ENSG00000116717	Chromatin interaction
ENSG00000163874	Chromatin interaction
ENSG00000187736	Chromatin interaction
ENSG00000233621	Chromatin interaction
ENSG00000272462	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1045537	1.00[ASN][1000 genomes]
rs10484433	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484435	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191445	0.82[EUR][1000 genomes]
rs13191776	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192365	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192713	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193424	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195279	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13195692	1.00[ASN][1000 genomes]
rs13196552	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13197334	1.00[ASN][1000 genomes]
rs13200797	1.00[ASN][1000 genomes]
rs13200888	1.00[ASN][1000 genomes]
rs13201821	1.00[ASN][1000 genomes]
rs13202371	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13202688	0.82[EUR][1000 genomes]
rs13203673	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206443	1.00[ASN][1000 genomes]
rs13206501	1.00[ASN][1000 genomes]
rs13207673	0.97[EUR][1000 genomes]
rs13210399	1.00[ASN][1000 genomes]
rs13212534	0.82[EUR][1000 genomes]
rs13214169	0.84[EUR][1000 genomes]
rs13214280	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13216785	1.00[ASN][1000 genomes]
rs13220395	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220488	0.97[EUR][1000 genomes]
rs16891235	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891261	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891264	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891315	1.00[ASN][1000 genomes]
rs16891334	1.00[ASN][1000 genomes]
rs17528178	0.82[EUR][1000 genomes]
rs17586553	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17586784	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17587226	0.93[EUR][1000 genomes]
rs17587597	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28360595	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34027471	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34116162	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34233736	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34525648	0.92[EUR][1000 genomes]
rs34791189	1.00[ASN][1000 genomes]
rs34804024	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35069699	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35116528	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35169013	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35249036	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35335639	1.00[ASN][1000 genomes]
rs35367169	0.90[ASN][1000 genomes]
rs35378061	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35402046	1.00[ASN][1000 genomes]
rs35484309	1.00[ASN][1000 genomes]
rs35528636	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35778245	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35825164	1.00[ASN][1000 genomes]
rs35902160	1.00[ASN][1000 genomes]
rs36012762	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3734523	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3734528	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3752417	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41266779	0.82[EUR][1000 genomes]
rs56195001	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56294283	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60512607	1.00[ASN][1000 genomes]
rs66790453	1.00[ASN][1000 genomes]
rs67296946	1.00[ASN][1000 genomes]
rs67491322	0.93[EUR][1000 genomes]
rs67844427	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs68149500	1.00[ASN][1000 genomes]
rs68194335	0.80[EUR][1000 genomes]
rs6903228	0.92[EUR][1000 genomes]
rs6931120	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6940007	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71557312	0.82[EUR][1000 genomes]
rs71557315	0.83[ASN][1000 genomes]
rs71557316	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72834617	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72834623	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748167	0.85[EUR][1000 genomes]
rs7749414	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750960	0.84[EUR][1000 genomes]
rs7766531	0.84[EUR][1000 genomes]
rs9295675	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9461222	0.92[EUR][1000 genomes]
rs9461223	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9467632	0.88[EUR][1000 genomes]
rs9467635	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	esv2755446	chr6:25924513-25981648	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv432857	chr6:25957109-26072445	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	451 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25956000-25963000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:25961600-25963000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:25961800-25963000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
4	chr6:25961800-25963000	Flanking Active TSS	Dnd41	blood
5	chr6:25962000-25963000	Enhancers	H9 Cell Line	embryonic stem cell
6	chr6:25962000-25963200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:25962000-25963200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:25962000-25963400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:25962000-25964000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:25962000-25964400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:25962000-25964800	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr6:25962200-25963000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr6:25962200-25964400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr6:25962200-25964400	Active TSS	Brain Anterior Caudate	brain
15	chr6:25962200-25964400	Active TSS	Brain Hippocampus Middle	brain
16	chr6:25962200-25964400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr6:25962200-25964800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:25962200-25965800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:25962400-25963000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr6:25962400-25963400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:25962400-25963800	Active TSS	Aorta	Aorta
22	chr6:25962400-25963800	Active TSS	Fetal Kidney	kidney
23	chr6:25962400-25964000	Active TSS	Gastric	stomach
24	chr6:25962400-25964200	Active TSS	Brain Angular Gyrus	brain
25	chr6:25962400-25964200	Active TSS	Brain Cingulate Gyrus	brain
26	chr6:25962400-25964200	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr6:25962400-25964200	Active TSS	Brain Substantia Nigra	brain
28	chr6:25962400-25964400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:25962400-25964400	Active TSS	Ovary	ovary
30	chr6:25962600-25963200	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr6:25962600-25963200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:25962600-25963200	Active TSS	Liver	Liver
33	chr6:25962600-25963400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr6:25962600-25963400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr6:25962600-25963400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
36	chr6:25962600-25963400	Bivalent/Poised TSS	HepG2	liver
37	chr6:25962600-25963400	Flanking Active TSS	NH-A	brain
38	chr6:25962600-25963800	Active TSS	Primary T cells fromperipheralblood	blood
39	chr6:25962600-25963800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr6:25962600-25963800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:25962600-25963800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:25962600-25963800	Active TSS	Colon Smooth Muscle	Colon
43	chr6:25962600-25963800	Active TSS	Psoas Muscle	Psoas
44	chr6:25962600-25963800	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr6:25962600-25964000	Active TSS	Pancreas	Pancrea
46	chr6:25962600-25964200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:25962600-25964200	Active TSS	Duodenum Mucosa	Duodenum
48	chr6:25962600-25964200	Active TSS	Esophagus	oesophagus
49	chr6:25962600-25964200	Active TSS	Thymus	Thymus
50	chr6:25962600-25964400	Active TSS	Colonic Mucosa	Colon

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