Variant report

Variant	rs56342784
Chromosome Location	chr6:27799332-27799333
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:368)
CpG islands
(count:122)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:368 , 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	POLR2A	chr6:27798229-27799532	NB4	blood:	n/a	n/a
2	SIN3AK20	chr6:27798918-27799619	HepG2	liver:	n/a	n/a
3	SP1	chr6:27798987-27799667	K562	blood:	n/a	chr6:27799416-27799428 chr6:27799429-27799440 chr6:27799426-27799440 chr6:27799416-27799427 chr6:27799417-27799426 chr6:27799430-27799439
4	NR2F2	chr6:27798166-27799777	K562	blood:	n/a	n/a
5	CHD2	chr6:27799322-27799771	K562	blood:	n/a	chr6:27799359-27799366
6	MAX	chr6:27799244-27799533	K562	blood:	n/a	n/a
7	REST	chr6:27798976-27799490	PFSK-1	brain:	n/a	n/a
8	TAF1	chr6:27798345-27799635	H1-hESC	embryonic stem cell:	n/a	n/a
9	CHD2	chr6:27798344-27799654	Hela-S3	cervix:	n/a	chr6:27799359-27799366
10	RUNX3	chr6:27799236-27799500	GM12878	blood:	n/a	n/a
11	GABPA	chr6:27799041-27799562	Hela-S3	cervix:	n/a	n/a
12	TAF1	chr6:27799229-27799500	K562	blood:	n/a	n/a
13	PAX5	chr6:27798100-27799610	GM12878	blood:	n/a	n/a
14	HCFC1	chr6:27799332-27799518	K562	blood:	n/a	n/a
15	ATF2	chr6:27799216-27799612	GM12878	blood:	n/a	n/a
16	USF1	chr6:27798959-27799446	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:27799242-27799513	HCT-116	colon:	n/a	n/a
18	MYBL2	chr6:27798318-27799892	HepG2	liver:	n/a	n/a
19	POU2F2	chr6:27798284-27799551	GM12878	blood:	n/a	n/a
20	USF1	chr6:27798940-27799517	HepG2	liver:	n/a	n/a
21	POLR2A	chr6:27796831-27799711	H1-hESC	embryonic stem cell:	n/a	n/a
22	YY1	chr6:27799252-27799405	GM12891	blood:	n/a	n/a
23	HEY1	chr6:27798181-27799703	HepG2	liver:	n/a	n/a
24	BCLAF1	chr6:27799198-27799812	K562	blood:	n/a	n/a
25	TAF1	chr6:27798923-27799505	GM12891	blood:	n/a	n/a
26	ZBTB33	chr6:27798521-27799524	GM12878	blood:	n/a	n/a
27	MYC	chr6:27798852-27799343	GM12878	blood:	n/a	n/a
28	POU2F2	chr6:27798413-27799548	GM12891	blood:	n/a	n/a
29	USF1	chr6:27799000-27799467	A549	lung:	n/a	n/a
30	TCF12	chr6:27798998-27799625	HepG2	liver:	n/a	chr6:27799455-27799462
31	POLR2A	chr6:27798058-27799530	GM12878	blood:	n/a	n/a
32	POLR2A	chr6:27798000-27799703	HepG2	liver:	n/a	n/a
33	EP300	chr6:27799178-27799714	A549	lung:	n/a	n/a
34	REST	chr6:27799214-27799556	A549	lung:	n/a	n/a
35	CEBPD	chr6:27799224-27799523	HepG2	liver:	n/a	n/a
36	NFIC	chr6:27798295-27799744	GM12878	blood:	n/a	n/a
37	MYC	chr6:27798909-27799397	MCF-7	breast:	n/a	n/a
38	POLR2A	chr6:27797760-27799531	GM12878	blood:	n/a	n/a
39	STAT3	chr6:27799283-27799545	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr6:27798372-27799480	HepG2	liver:	n/a	n/a
41	CTCF	chr6:27799118-27799367	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:27798291-27799523	GM12878	blood:	n/a	n/a
43	CHD2	chr6:27799159-27799540	GM12878	blood:	n/a	chr6:27799359-27799366
44	EP300	chr6:27799323-27799531	GM12878	blood:	n/a	n/a
45	REST	chr6:27799100-27799462	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr6:27798215-27799532	Hela-S3	cervix:	n/a	n/a
47	ZBTB33	chr6:27798589-27799657	HepG2	liver:	n/a	n/a
48	SIN3AK20	chr6:27799127-27799474	A549	lung:	n/a	n/a
49	TCF3	chr6:27798386-27799520	GM12878	blood:	n/a	n/a
50	STAT3	chr6:27799301-27799636	MCF10A-Er-Src	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:27799308-27799358	GM19239	blood:	n/a
2	chr6:27799295-27799345	GM06990	blood:	n/a
3	chr6:27799295-27799345	NT2-D1	testis:	n/a
4	chr6:27799308-27799358	HRCEpiC	kidney:	n/a
5	chr6:27799295-27799345	HCT-116	colon:	n/a
6	chr6:27799308-27799358	SAEC	small airway:	n/a
7	chr6:27799295-27799345	SKMC	muscle:	n/a
8	chr6:27799308-27799358	NHBE	bronchial:	n/a
9	chr6:27799295-27799345	AG10803	skin:	n/a
10	chr6:27799308-27799358	HRPEpiC	eye:	n/a
11	chr6:27799308-27799358	HL-60	blood:	n/a
12	chr6:27799295-27799345	HUVEC	blood vessel:	n/a
13	chr6:27799295-27799345	HAEpiC	amniotic membrane:	n/a
14	chr6:27799295-27799345	Jurkat	blood:	n/a
15	chr6:27799308-27799358	PrEC	prostate:	n/a
16	chr6:27799295-27799345	AG09309	skin:	n/a
17	chr6:27799295-27799345	ovcar-3	ovarian:	n/a
18	chr6:27799295-27799345	GM12878	blood:	n/a
19	chr6:27799308-27799358	HCPEpiC	choroid plexus:	n/a
20	chr6:27799295-27799345	NH-A	brain:	n/a
21	chr6:27799308-27799358	GM06990	blood:	n/a
22	chr6:27799295-27799345	HCF	heart:	n/a
23	chr6:27799308-27799358	RPTEC	kidney:	n/a
24	chr6:27799295-27799345	Hela-S3	cervix:	n/a
25	chr6:27799295-27799345	HL-60	blood:	n/a
26	chr6:27799295-27799345	NHBE	bronchial:	n/a
27	chr6:27799308-27799358	LNCaP	prostate:	n/a
28	chr6:27799295-27799345	AG04450	lung:	fetal
29	chr6:27799295-27799345	PrEC	prostate:	n/a
30	chr6:27799295-27799345	GM19239	blood:	n/a
31	chr6:27799308-27799358	HCF	heart:	n/a
32	chr6:27799308-27799358	HEEpiC	esophagus:	n/a
33	chr6:27799308-27799358	H1-hESC	embryonic stem cell:	embryo
34	chr6:27799295-27799345	PANC-1	pancreas:	n/a
35	chr6:27799308-27799358	AG04449	skin:	fetal
36	chr6:27799295-27799345	NB4	blood:	n/a
37	chr6:27799308-27799358	NHDF-neo	bronchial:	n/a
38	chr6:27799295-27799345	H1-hESC	embryonic stem cell:	embryo
39	chr6:27799295-27799345	MCF10A-Er-Src	breast:	n/a
40	chr6:27799308-27799358	AG09319	gingival:	n/a
41	chr6:27799308-27799358	PANC-1	pancreas:	n/a
42	chr6:27799308-27799358	HPAEpiC	pulmonary alveolar:	n/a
43	chr6:27799308-27799358	SK-N-SH	brain:	n/a
44	chr6:27799295-27799345	AG04449	skin:	fetal
45	chr6:27799295-27799345	SK-N-SH_RA	brain:	n/a
46	chr6:27799308-27799358	NB4	blood:	n/a
47	chr6:27799295-27799345	SK-N-MC	brain:	n/a
48	chr6:27799295-27799345	IMR90	lung:	fetal
49	chr6:27799308-27799358	NT2-D1	testis:	n/a
50	chr6:27799308-27799358	ECC-1	luminal epithelium:	n/a

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27796630..27800125-chr6:28302655..28305022,3	K562	blood:
2	chr1:150121553..150123075-chr6:27798165..27799927,2	MCF-7	breast:
3	chr6:27798954..27801175-chr6:28191953..28194580,2	K562	blood:
4	chr6:27104100..27108145-chr6:27797427..27800059,3	K562	blood:
5	chr6:26155325..26157964-chr6:27797146..27799688,3	MCF-7	breast:
6	chr6:27797717..27799808-chr9:127629757..127631967,2	K562	blood:
7	chr6:26187875..26189403-chr6:27797113..27800006,2	MCF-7	breast:
8	chr6:26053058..26056960-chr6:27797302..27800295,3	MCF-7	breast:
9	chr6:27798350..27799895-chr6:34855095..34857385,2	K562	blood:
10	chr6:27796980..27799834-chr6:28103780..28105751,2	K562	blood:
11	chr6:27098287..27103463-chr6:27796109..27800380,7	K562	blood:
12	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
13	chr6:26122973..26125036-chr6:27798042..27800567,2	MCF-7	breast:
14	chr6:27798054..27799666-chr7:102036106..102037763,2	MCF-7	breast:
15	chr6:27798199..27799834-chr6:28104251..28105914,2	K562	blood:
16	chr6:27782776..27783687-chr6:27798847..27799701,2	NB4	blood:
17	chr6:26025221..26028451-chr6:27796635..27801025,4	K562	blood:
18	chr6:27217724..27219322-chr6:27799079..27801494,2	MCF-7	breast:
19	chr14:23387918..23388718-chr6:27798376..27799339,2	Hela-S3	cervix:
20	chr6:26025403..26028129-chr6:27797100..27800385,4	MCF-7	breast:
21	chr6:27113131..27119021-chr6:27794877..27801018,12	K562	blood:
22	chr6:27798534..27801249-chrX:16803484..16805157,2	MCF-7	breast:
23	chr14:93673121..93674052-chr6:27798856..27799361,2	Hela-S3	cervix:
24	chr6:26251146..26253311-chr6:27798112..27799639,2	MCF-7	breast:
25	chr6:27798625..27800434-chr6:28302917..28305015,2	K562	blood:

No data

Variant related genes	Relation type
HIST1H4K	TF binding region
HIST1H4K	CpG island
ENSG00000124529	Chromatin interaction
ENSG00000086712	Chromatin interaction
ENSG00000170270	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000064999	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000237054	Chromatin interaction
ENSG00000064995	Chromatin interaction
ENSG00000012963	Chromatin interaction
ENSG00000128563	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000100461	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000188987	Chromatin interaction
ENSG00000136950	Chromatin interaction
ENSG00000112812	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000197459	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000184825	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs187995	1.00[EUR][1000 genomes]
rs200470	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200472	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200947	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200955	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200959	1.00[EUR][1000 genomes]
rs200982	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200984	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs201003	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs201005	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59716769	1.00[EUR][1000 genomes]
rs7740062	1.00[EUR][1000 genomes]
rs9468198	1.00[EUR][1000 genomes]
rs9468205	1.00[EUR][1000 genomes]
rs9468228	0.89[AMR][1000 genomes];1.00[EUR][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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
5	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27793400-27803200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:27797200-27799600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:27797200-27799600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:27797200-27799600	Active TSS	Brain Germinal Matrix	brain
5	chr6:27797200-27799800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr6:27797400-27799400	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:27797400-27799600	Active TSS	H1 Cell Line	embryonic stem cell
8	chr6:27797400-27799600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr6:27797400-27799800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:27797600-27799600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr6:27797600-27799600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:27797600-27799600	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr6:27797600-27799600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr6:27797600-27799600	Active TSS	Thymus	Thymus
15	chr6:27797600-27799800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:27797600-27799800	Active TSS	Rectal Smooth Muscle	rectum
17	chr6:27797600-27799800	Active TSS	HMEC	breast
18	chr6:27797600-27799800	Active TSS	NHLF	lung
19	chr6:27797800-27799600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:27797800-27799800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:27797800-27799800	Active TSS	Brain Anterior Caudate	brain
22	chr6:27797800-27799800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:27797800-27799800	Active TSS	Fetal Intestine Large	intestine
24	chr6:27797800-27799800	Active TSS	Stomach Smooth Muscle	stomach
25	chr6:27797800-27800200	Active TSS	GM12878-XiMat	blood
26	chr6:27798000-27799600	Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr6:27798000-27799600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:27798000-27799800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:27798000-27799800	Active TSS	Fetal Thymus	thymus
30	chr6:27798000-27799800	Active TSS	NHDF-Ad	bronchial
31	chr6:27798200-27799600	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr6:27798200-27799600	Active TSS	Brain Substantia Nigra	brain
33	chr6:27798200-27799600	Active TSS	Hela-S3	cervix
34	chr6:27798200-27799600	Active TSS	HSMM	muscle
35	chr6:27798200-27799800	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr6:27798200-27799800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
37	chr6:27798200-27799800	Active TSS	Fetal Muscle Trunk	muscle
38	chr6:27798400-27799400	Transcr. at gene 5' and 3'	Right Atrium	heart
39	chr6:27798400-27799600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:27798400-27799600	Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr6:27798400-27799600	Active TSS	Aorta	Aorta
42	chr6:27798400-27799600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
43	chr6:27798400-27799600	Active TSS	Stomach Mucosa	stomach
44	chr6:27798400-27799800	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr6:27798400-27799800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:27798400-27799800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:27798400-27799800	Active TSS	HSMMtube	muscle
48	chr6:27798600-27799600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:27798600-27799600	Active TSS	Fetal Kidney	kidney
50	chr6:27798600-27799600	Active TSS	Placenta Amnion	Placenta Amnion

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