Variant report

Variant	rs1061625
Chromosome Location	chr6:28891458-28891459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:364)
CpG islands
(count:183)
Chromatin interactive
region (count:30)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:364 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr6:28891421-28892016	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr6:28890685-28892073	GM12878	blood:	n/a	n/a
3	SP1	chr6:28891404-28892044	A549	lung:	n/a	chr6:28891799-28891811 chr6:28891800-28891810 chr6:28891800-28891810 chr6:28891801-28891810 chr6:28891800-28891809 chr6:28891801-28891810 chr6:28891799-28891811 chr6:28891765-28891775
4	HA-E2F1	chr6:28890604-28892095	MCF-7	breast:	n/a	chr6:28891750-28891760 chr6:28890907-28890921 chr6:28891800-28891809 chr6:28890959-28890971
5	POLR2A	chr6:28890484-28892149	ECC-1	luminal epithelium:	n/a	n/a
6	CTCF	chr6:28891217-28891827	K562	blood:	n/a	n/a
7	NR2F2	chr6:28889743-28892578	K562	blood:	n/a	n/a
8	SIN3AK20	chr6:28891094-28892102	HepG2	liver:	n/a	n/a
9	MYBL2	chr6:28890481-28892204	HepG2	liver:	n/a	n/a
10	POLR2A	chr6:28889875-28892268	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr6:28890358-28892615	K562	blood:	n/a	n/a
12	SMARCC1	chr6:28890501-28892027	Hela-S3	cervix:	n/a	n/a
13	MYBL2	chr6:28891341-28892145	HepG2	liver:	n/a	n/a
14	HCFC1	chr6:28890274-28892322	Hela-S3	cervix:	n/a	n/a
15	TAF7	chr6:28891275-28892081	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr6:28891440-28891590	HMEC	breast:	n/a	n/a
17	GABPA	chr6:28890768-28892170	K562	blood:	n/a	chr6:28891800-28891809
18	CTCF	chr6:28891380-28891530	Hela-S3	cervix:	n/a	n/a
19	GABPA	chr6:28891333-28892089	SK-N-SH	brain:	n/a	chr6:28891800-28891809
20	POLR2A	chr6:28891257-28892121	SK-N-MC	brain:	n/a	n/a
21	CTCF	chr6:28891420-28891570	NHEK	skin:	n/a	n/a
22	TBL1XR1	chr6:28891453-28891978	K562	blood:	n/a	n/a
23	ATF2	chr6:28890723-28891520	GM12878	blood:	n/a	n/a
24	POLR2A	chr6:28890690-28892256	HepG2	liver:	n/a	n/a
25	POLR2A	chr6:28890756-28892067	A549	lung:	n/a	n/a
26	FOXM1	chr6:28891451-28892007	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:28890378-28892039	GM12891	blood:	n/a	n/a
28	BHLHE40	chr6:28890684-28892055	GM12878	blood:	n/a	chr6:28891990-28892006 chr6:28891987-28892003
29	MYC	chr6:28890871-28891928	MCF-7	breast:	n/a	n/a
30	PML	chr6:28889740-28892185	K562	blood:	n/a	chr6:28890027-28890036
31	CTCF	chr6:28891360-28891510	HEK293	kidney:	n/a	n/a
32	CREB1	chr6:28891290-28892125	GM12878	blood:	n/a	n/a
33	MXI1	chr6:28889872-28892194	IMR90	lung:	n/a	n/a
34	POLR2A	chr6:28889681-28892110	K562	blood:	n/a	n/a
35	MYC	chr6:28890853-28892001	MCF-7	breast:	n/a	n/a
36	POLR2A	chr6:28889280-28892096	K562	blood:	n/a	n/a
37	ZNF143	chr6:28890813-28892004	GM12878	blood:	n/a	n/a
38	CTCF	chr6:28891400-28891550	Caco-2	colon:	n/a	n/a
39	CTCF	chr6:28891320-28891470	WERI-Rb-1	eye:	n/a	n/a
40	NFIC	chr6:28891266-28892189	GM12878	blood:	n/a	n/a
41	TAL1	chr6:28890861-28891922	K562	blood:	n/a	n/a
42	POLR2A	chr6:28890796-28892070	H1-hESC	embryonic stem cell:	n/a	n/a
43	RAD21	chr6:28891433-28891518	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr6:28890925-28892103	HEK293	kidney:	n/a	n/a
45	CTCF	chr6:28891400-28891550	SK-N-SH_RA	brain:	n/a	n/a
46	ZNF263	chr6:28889915-28892045	HEK293-T-REx	kidney:	n/a	n/a
47	MAX	chr6:28890653-28892072	GM12878	blood:	n/a	n/a
48	CCNT2	chr6:28890492-28892028	K562	blood:	n/a	chr6:28891766-28891775 chr6:28890781-28890790 chr6:28891800-28891809
49	POLR2A	chr6:28889873-28892186	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr6:28890298-28892108	GM15510	blood:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28891451-28891501	NHDF-neo	bronchial:	n/a
2	chr6:28891412-28891462	AG04450	lung:	fetal
3	chr6:28891412-28891462	BE2_C	brain:	n/a
4	chr6:28891412-28891462	BJ	skin:	n/a
5	chr6:28891451-28891501	HCM	heart:	n/a
6	chr6:28891451-28891501	A549	lung:	n/a
7	chr6:28891451-28891501	BJ	skin:	n/a
8	chr6:28891412-28891462	K562	blood:	n/a
9	chr6:28891412-28891462	PANC-1	pancreas:	n/a
10	chr6:28891412-28891462	HUVEC	blood vessel:	n/a
11	chr6:28891412-28891462	HEEpiC	esophagus:	n/a
12	chr6:28891412-28891462	T-47D	breast:	n/a
13	chr6:28891451-28891501	PFSK-1	brain:	n/a
14	chr6:28891451-28891501	H1-hESC	embryonic stem cell:	embryo
15	chr6:28891448-28891498	Caco-2	colon:	n/a
16	chr6:28891412-28891462	ovcar-3	ovarian:	n/a
17	chr6:28891451-28891501	SKMC	muscle:	n/a
18	chr6:28891448-28891498	HRCEpiC	kidney:	n/a
19	chr6:28891451-28891501	Caco-2	colon:	n/a
20	chr6:28891412-28891462	HAEpiC	amniotic membrane:	n/a
21	chr6:28891451-28891501	NB4	blood:	n/a
22	chr6:28891412-28891462	MCF10A-Er-Src	breast:	n/a
23	chr6:28891451-28891501	ovcar-3	ovarian:	n/a
24	chr6:28891451-28891501	NHBE	bronchial:	n/a
25	chr6:28891448-28891498	NB4	blood:	n/a
26	chr6:28891412-28891462	PFSK-1	brain:	n/a
27	chr6:28891448-28891498	HIPEpiC	eye:	n/a
28	chr6:28891412-28891462	HMEC	breast:	n/a
29	chr6:28891448-28891498	BJ	skin:	n/a
30	chr6:28891448-28891498	Hela-S3	cervix:	n/a
31	chr6:28891451-28891501	AG09319	gingival:	n/a
32	chr6:28891412-28891462	HCPEpiC	choroid plexus:	n/a
33	chr6:28891448-28891498	SAEC	small airway:	n/a
34	chr6:28891412-28891462	Jurkat	blood:	n/a
35	chr6:28891412-28891462	RPTEC	kidney:	n/a
36	chr6:28891412-28891462	NB4	blood:	n/a
37	chr6:28891412-28891462	NHDF-neo	bronchial:	n/a
38	chr6:28891448-28891498	HCT-116	colon:	n/a
39	chr6:28891448-28891498	AG09319	gingival:	n/a
40	chr6:28891412-28891462	PrEC	prostate:	n/a
41	chr6:28891451-28891501	HCF	heart:	n/a
42	chr6:28891451-28891501	Hela-S3	cervix:	n/a
43	chr6:28891448-28891498	HPAEpiC	pulmonary alveolar:	n/a
44	chr6:28891448-28891498	HCM	heart:	n/a
45	chr6:28891448-28891498	AG09309	skin:	n/a
46	chr6:28891412-28891462	AG04449	skin:	fetal
47	chr6:28891412-28891462	GM12878	blood:	n/a
48	chr6:28891412-28891462	HEK293	kidney:	embryo
49	chr6:28891451-28891501	AG09309	skin:	n/a
50	chr6:28891448-28891498	SKMC	muscle:	n/a

(count:30 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28887886..28894013-chr6:28935014..28940220,8	K562	blood:
2	chr6:28808787..28809525-chr6:28890975..28891547,2	MCF-7	breast:
3	chr6:28831130..28836886-chr6:28890033..28892870,9	MCF-7	breast:
4	chr6:28889368..28892748-chr6:28952347..28956108,5	MCF-7	breast:
5	chr6:28861677..28871493-chr6:28888734..28892704,20	MCF-7	breast:
6	chr6:28874441..28877573-chr6:28886876..28891614,6	MCF-7	breast:
7	chr6:28890449..28893259-chr6:28971754..28975345,6	K562	blood:
8	chr1:198126086..198126981-chr6:28891160..28891856,2	Hela-S3	cervix:
9	chr1:91486430..91487378-chr6:28891311..28892063,2	Hela-S3	cervix:
10	chr6:28889372..28892274-chr6:28936954..28941148,4	K562	blood:
11	chr6:28889101..28891643-chr6:29595051..29597893,2	K562	blood:
12	chr6:28890727..28894097-chr6:28943047..28947323,5	MCF-7	breast:
13	chr6:28831640..28835125-chr6:28890004..28893108,3	MCF-7	breast:
14	chr6:28874958..28881784-chr6:28883001..28892669,21	MCF-7	breast:
15	chr6:28882946..28884920-chr6:28890308..28891920,2	MCF-7	breast:
16	chr6:28861810..28871966-chr6:28889574..28894668,20	MCF-7	breast:
17	chr6:28888957..28894217-chr6:28902105..28913114,27	MCF-7	breast:
18	chr6:28805285..28808440-chr6:28888511..28892745,5	K562	blood:
19	chr6:28886838..28893375-chr6:28904762..28912890,19	K562	blood:
20	chr1:115300126..115300808-chr6:28891450..28892062,2	Hela-S3	cervix:
21	chr6:27856359..27859269-chr6:28891133..28894008,2	MCF-7	breast:
22	chr6:27776463..27779000-chr6:28890031..28892525,2	MCF-7	breast:
23	chr6:28891456..28893478-chr6:28954362..28956726,2	K562	blood:
24	chr6:28890160..28893119-chr6:28970726..28976038,6	K562	blood:
25	chr6:28805285..28809041-chr6:28890242..28892830,8	K562	blood:
26	chr6:28831633..28833233-chr6:28890419..28893119,2	K562	blood:
27	chr6:28856776..28858832-chr6:28890243..28892379,2	MCF-7	breast:
28	chr17:19551796..19552380-chr6:28891386..28892119,2	HCT-116	colon:
29	chr6:27831507..27834483-chr6:28890233..28891763,2	MCF-7	breast:
30	chr6:28804571..28808832-chr6:28889803..28892525,4	MCF-7	breast:

No data

Variant related genes	Relation type
TRIM27	TF binding region
TRIM27	CpG island
ENSG00000263426	Chromatin interaction
ENSG00000009307	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000151414	Chromatin interaction
ENSG00000233366	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000072210	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000212240	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000244349	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000217646	Chromatin interaction
ENSG00000204681	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000198374	Chromatin interaction
ENSG00000228666	Chromatin interaction
ENSG00000122482	Chromatin interaction
ENSG00000225595	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs172326	0.89[ASN][1000 genomes]
rs1794588	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs184094	0.83[ASN][1000 genomes]
rs209127	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs209140	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209147	0.86[ASN][1000 genomes]
rs209151	0.87[ASN][1000 genomes]
rs209165	0.84[ASN][1000 genomes]
rs209172	0.83[ASN][1000 genomes]
rs209177	0.85[ASN][1000 genomes]
rs209180	0.81[ASN][1000 genomes]
rs2097424	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2148007	0.82[ASN][1000 genomes]
rs2269553	0.88[ASN][1000 genomes]
rs2894066	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3130843	0.89[ASN][1000 genomes]
rs3131067	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3131098	0.80[ASN][1000 genomes]
rs3132377	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132380	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3135314	0.81[ASN][1000 genomes]
rs393309	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs413972	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs422331	0.84[ASN][1000 genomes]
rs429369	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4484511	0.81[ASN][1000 genomes]
rs6906953	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6912843	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6926892	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7740125	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7750338	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7769221	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs876737	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9257280	0.81[ASN][1000 genomes]
rs9257328	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9257395	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9257399	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9257412	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9257416	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9257425	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs929042	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv601212	chr6:28833225-28893927	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription 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	47 gene(s)	inside rSNPs	diseases
5	nsv462667	chr6:28834646-28893927	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28889800-28892400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:28889800-28892600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:28890000-28892200	Active TSS	Aorta	Aorta
4	chr6:28890000-28892200	Active TSS	Fetal Intestine Small	intestine
5	chr6:28890000-28892400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:28890000-28892400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:28890000-28892400	Active TSS	Colonic Mucosa	Colon
8	chr6:28890000-28892400	Active TSS	Fetal Intestine Large	intestine
9	chr6:28890000-28892600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr6:28890000-28892600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:28890000-28892600	Active TSS	Lung	lung
12	chr6:28890000-28892600	Active TSS	Pancreas	Pancrea
13	chr6:28890000-28892600	Active TSS	Psoas Muscle	Psoas
14	chr6:28890000-28892800	Active TSS	H9 Cell Line	embryonic stem cell
15	chr6:28890000-28892800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:28890200-28891800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:28890200-28892000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr6:28890200-28892000	Active TSS	Fetal Muscle Trunk	muscle
19	chr6:28890200-28892000	Active TSS	Stomach Mucosa	stomach
20	chr6:28890200-28892200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:28890200-28892200	Active TSS	Ovary	ovary
22	chr6:28890200-28892200	Active TSS	NHDF-Ad	bronchial
23	chr6:28890200-28892400	Active TSS	H1 Cell Line	embryonic stem cell
24	chr6:28890200-28892400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:28890200-28892400	Active TSS	GM12878-XiMat	blood
26	chr6:28890200-28892400	Active TSS	NHLF	lung
27	chr6:28890200-28892600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr6:28890200-28892600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:28890200-28892600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:28890200-28892600	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr6:28890200-28892600	Active TSS	A549	lung
32	chr6:28890200-28892800	Active TSS	HSMMtube	muscle
33	chr6:28890200-28893000	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr6:28890400-28891600	Bivalent/Poised TSS	HepG2	liver
35	chr6:28890400-28891800	Active TSS	Fetal Heart	heart
36	chr6:28890400-28892200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr6:28890400-28892200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:28890400-28892200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:28890400-28892200	Active TSS	Gastric	stomach
40	chr6:28890400-28892200	Active TSS	Placenta Amnion	Placenta Amnion
41	chr6:28890400-28892200	Active TSS	Small Intestine	intestine
42	chr6:28890400-28892200	Active TSS	Thymus	Thymus
43	chr6:28890400-28892400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr6:28890400-28892400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:28890400-28892400	Active TSS	Fetal Stomach	stomach
46	chr6:28890400-28892400	Active TSS	Right Ventricle	heart
47	chr6:28890400-28892400	Active TSS	Osteobl	bone
48	chr6:28890400-28892600	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr6:28890400-28892600	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr6:28890400-28892600	Active TSS	Left Ventricle	heart

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