Variant report

Variant	rs3873304
Chromosome Location	chr6:30586031-30586032
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	MTA3	chr6:30585276-30586161	GM12878	blood:	n/a	n/a
2	TEAD4	chr6:30581902-30586732	K562	blood:	n/a	n/a
3	ATF2	chr6:30582186-30586052	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:30576348-30586731	PANC-1	pancreas:	n/a	n/a
5	RELA	chr6:30583723-30586302	GM15510	blood:	n/a	n/a
6	POLR2A	chr6:30579350-30586587	HUVEC	blood vessel:	n/a	n/a
7	NFIC	chr6:30582006-30586341	HepG2	liver:	n/a	n/a
8	MBD4	chr6:30585188-30586510	HepG2	liver:	n/a	n/a
9	MAX	chr6:30584325-30586309	HCT-116	colon:	n/a	chr6:30585856-30585866
10	TBL1XR1	chr6:30582113-30586538	K562	blood:	n/a	n/a
11	POLR2A	chr6:30579823-30586558	K562	blood:	n/a	n/a
12	NFIC	chr6:30581686-30586080	GM12878	blood:	n/a	n/a
13	MAX	chr6:30584410-30586094	MCF-7	breast:	n/a	chr6:30585856-30585866
14	NR2F2	chr6:30584475-30586431	K562	blood:	n/a	n/a
15	POLR2A	chr6:30576459-30586534	MCF10A-Er-Src	breast:	n/a	n/a
16	YY1	chr6:30584705-30586069	H1-hESC	embryonic stem cell:	n/a	chr6:30585024-30585038 chr6:30584843-30584851
17	GABPA	chr6:30584674-30586166	A549	lung:	n/a	chr6:30585334-30585348 chr6:30585591-30585605 chr6:30585337-30585346 chr6:30585337-30585348 chr6:30585337-30585351 chr6:30585238-30585247 chr6:30585591-30585602 chr6:30585339-30585348
18	MYBL2	chr6:30581783-30586375	HepG2	liver:	n/a	n/a
19	MAX	chr6:30584549-30586265	NB4	blood:	n/a	chr6:30585856-30585866
20	PML	chr6:30579632-30586566	GM12878	blood:	n/a	chr6:30580599-30580607
21	POLR2A	chr6:30576762-30586531	Hela-S3	cervix:	n/a	n/a
22	FOXM1	chr6:30581121-30586310	GM12878	blood:	n/a	n/a
23	MXI1	chr6:30584301-30586720	IMR90	lung:	n/a	n/a
24	POLR2A	chr6:30580395-30586632	GM12892	blood:	n/a	n/a
25	MYC	chr6:30584557-30586421	K562	blood:	n/a	chr6:30585856-30585866
26	YY1	chr6:30584421-30586062	K562	blood:	n/a	chr6:30585024-30585038 chr6:30584843-30584851
27	MAX	chr6:30584778-30586215	SK-N-SH	brain:	n/a	chr6:30585856-30585866
28	POLR2A	chr6:30576843-30586279	HCT-116	colon:	n/a	n/a
29	FOS	chr6:30584766-30586065	K562	blood:	n/a	chr6:30585855-30585864
30	STAT5A	chr6:30580246-30586275	GM12878	blood:	n/a	chr6:30585223-30585231 chr6:30580358-30580365 chr6:30583348-30583356 chr6:30583199-30583211 chr6:30582085-30582096 chr6:30582020-30582028
31	MAX	chr6:30584669-30586084	MCF-7	breast:	n/a	chr6:30585856-30585866
32	POLR2A	chr6:30576894-30586563	PANC-1	pancreas:	n/a	n/a
33	POLR2A	chr6:30579091-30586493	GM12878	blood:	n/a	n/a
34	STAT3	chr6:30584741-30586149	GM12878	blood:	n/a	chr6:30585223-30585231
35	YY1	chr6:30584638-30586048	HepG2	liver:	n/a	chr6:30585024-30585038 chr6:30584843-30584851
36	EP300	chr6:30584365-30586038	ECC-1	luminal epithelium:	n/a	chr6:30585172-30585186
37	POLR2A	chr6:30576267-30586793	SK-N-MC	brain:	n/a	n/a
38	IRF1	chr6:30581544-30586380	K562	blood:	n/a	chr6:30582594-30582611 chr6:30585161-30585170 chr6:30582597-30582611 chr6:30582591-30582605 chr6:30584185-30584198 chr6:30582036-30582056 chr6:30582587-30582607 chr6:30582085-30582096 chr6:30583087-30583104 chr6:30582592-30582609 chr6:30582595-30582609 chr6:30582595-30582606 chr6:30585184-30585198 chr6:30582085-30582095 chr6:30582592-30582606 chr6:30582595-30582605 chr6:30582081-30582095 chr6:30582593-30582606 chr6:30582083-30582096
39	TBP	chr6:30584617-30586458	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr6:30582009-30586107	HL-60	blood:	n/a	n/a
41	ETS1	chr6:30584750-30586037	GM12878	blood:	n/a	chr6:30585285-30585295 chr6:30585287-30585296 chr6:30585855-30585866 chr6:30585098-30585107 chr6:30585838-30585852 chr6:30585835-30585852
42	MAX	chr6:30584544-30586061	SK-N-SH	brain:	n/a	chr6:30585856-30585866
43	POLR2A	chr6:30579994-30586398	K562	blood:	n/a	n/a
44	YY1	chr6:30584660-30586070	ECC-1	luminal epithelium:	n/a	chr6:30585024-30585038 chr6:30584843-30584851
45	GABPA	chr6:30584367-30586224	MCF-7	breast:	n/a	chr6:30585334-30585348 chr6:30585591-30585605 chr6:30585337-30585346 chr6:30585337-30585348 chr6:30585337-30585351 chr6:30585238-30585247 chr6:30585591-30585602 chr6:30585339-30585348
46	POLR2A	chr6:30576421-30586088	SK-N-SH	brain:	n/a	n/a
47	HEY1	chr6:30581061-30586645	K562	blood:	n/a	n/a
48	POLR2A	chr6:30581594-30586552	Hela-S3	cervix:	n/a	n/a
49	MYBL2	chr6:30580829-30586221	HepG2	liver:	n/a	n/a
50	MYC	chr6:30584413-30586550	K562	blood:	n/a	chr6:30585856-30585866

No.	Distal block	Cell Line	Cell type
1	chr6:30580498..30587281-chr6:30649167..30662031,51	K562	blood:
2	chr6:30577773..30589670-chr6:30680333..30700280,58	MCF-7	breast:
3	chr6:30585676..30586235-chr9:19379373..19380163,2	NB4	blood:
4	chr6:30293494..30295921-chr6:30584661..30586515,2	K562	blood:
5	chr6:30583697..30586292-chr6:30616781..30618296,2	MCF-7	breast:
6	chr6:30585321..30586075-chr6:35419788..35420370,2	HCT-116	colon:
7	chr6:30581806..30587588-chr6:30850201..30854112,13	MCF-7	breast:
8	chr6:30455822..30466395-chr6:30579571..30587610,27	K562	blood:
9	chr17:56709009..56710623-chr6:30584971..30586605,2	MCF-7	breast:
10	chr6:30580645..30587403-chr6:30708153..30714600,16	MCF-7	breast:
11	chr6:30577862..30587208-chr6:30682997..30696247,43	MCF-7	breast:
12	chr3:154041803..154042377-chr6:30585398..30586111,2	NB4	blood:
13	chr16:87984268..87986838-chr6:30583707..30586082,2	MCF-7	breast:
14	chr6:30582891..30586139-chr6:30656870..30660301,3	MCF-7	breast:
15	chr6:30577127..30589352-chr6:30620628..30648657,88	K562	blood:
16	chr6:30452366..30463564-chr6:30577885..30586736,19	MCF-7	breast:
17	chr6:30537301..30541414-chr6:30578056..30586798,20	MCF-7	breast:
18	chr6:30581875..30586807-chr6:30843879..30846748,7	K562	blood:
19	chr6:30583409..30587215-chr6:30748473..30750740,4	K562	blood:
20	chr6:30583713..30586617-chr6:30879172..30881064,2	MCF-7	breast:
21	chr6:30520810..30527475-chr6:30577152..30588201,32	MCF-7	breast:
22	chr6:30293501..30295806-chr6:30583692..30586477,2	MCF-7	breast:
23	chr6:30584082..30586982-chr6:30608127..30610003,2	MCF-7	breast:
24	chr6:26020054..26021608-chr6:30585009..30586563,2	K562	blood:
25	chr6:30585114..30586870-chr6:31632529..31634643,2	K562	blood:
26	chr11:62359162..62361796-chr6:30583818..30586376,2	K562	blood:
27	chr6:30312149..30313971-chr6:30583567..30587070,3	K562	blood:
28	chr12:120727070..120730888-chr6:30582965..30586622,3	MCF-7	breast:
29	chr6:30293720..30295941-chr6:30584263..30586313,2	K562	blood:
30	chr6:30580789..30587552-chr6:30608606..30620072,66	K562	blood:
31	chr6:26030782..26033765-chr6:30585161..30587515,2	MCF-7	breast:
32	chr6:30576582..30588788-chr6:30682721..30700088,114	K562	blood:
33	chr6:30581846..30586345-chr6:30599769..30603372,4	MCF-7	breast:
34	chr6:30431634..30435485-chr6:30582972..30586314,3	K562	blood:
35	chr6:30585269..30586169-chr9:131314423..131315415,2	Hela-S3	cervix:
36	chr6:30581230..30587315-chr6:30638443..30644329,12	MCF-7	breast:
37	chr6:30581322..30587794-chr6:30705649..30714068,32	K562	blood:
38	chr6:30517868..30527565-chr6:30576812..30587078,24	MCF-7	breast:
39	chr6:30584033..30586510-chr6:31124123..31126779,2	K562	blood:
40	chr6:30583545..30586231-chr6:30734562..30736210,2	K562	blood:
41	chr6:30579823..30587267-chr6:30636296..30642513,15	MCF-7	breast:
42	chr6:30482489..30485588-chr6:30582296..30586114,5	K562	blood:
43	chr6:26155518..26157248-chr6:30585019..30587976,2	K562	blood:
44	chr6:30582201..30587134-chr6:30612921..30616733,15	MCF-7	breast:
45	chr1:149857493..149860440-chr6:30582683..30586274,4	MCF-7	breast:

Variant related genes	Relation type
PPP1R10	TF binding region
ENSG00000222894	TF binding region
ENSG00000137343	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000172530	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000272540	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000229068	Chromatin interaction
ENSG00000228415	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000266183	Chromatin interaction
ENSG00000213780	Chromatin interaction
ENSG00000112039	Chromatin interaction
ENSG00000228022	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000204592	Chromatin interaction
ENSG00000137404	Chromatin interaction
ENSG00000146112	Chromatin interaction
ENSG00000204536	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000174953	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000137310	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000197694	Chromatin interaction
ENSG00000228395	Chromatin interaction
ENSG00000235781	Chromatin interaction
ENSG00000204574	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000204564	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000204599	Chromatin interaction
ENSG00000196230	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000241370	Chromatin interaction
ENSG00000236603	Chromatin interaction
ENSG00000231074	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000204438	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11965214	0.83[ASN][1000 genomes]
rs28986316	0.83[ASN][1000 genomes]
rs28986317	0.83[ASN][1000 genomes]
rs34890315	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41315800	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
4	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
5	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
6	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
7	nsv884091	chr6:30526026-30590646	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	776 gene(s)	inside rSNPs	diseases
8	nsv5244	chr6:30545111-30589803	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	772 gene(s)	inside rSNPs	diseases
9	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 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	chr6:30581800-30586600	Active TSS	Right Ventricle	heart
2	chr6:30582000-30586600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:30582200-30586400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr6:30582200-30586400	Active TSS	Esophagus	oesophagus
5	chr6:30582200-30586400	Active TSS	Lung	lung
6	chr6:30582200-30586400	Active TSS	Ovary	ovary
7	chr6:30582400-30586600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:30582400-30586600	Active TSS	Gastric	stomach
9	chr6:30582400-30586800	Active TSS	Psoas Muscle	Psoas
10	chr6:30582600-30586200	Active TSS	Placenta Amnion	Placenta Amnion
11	chr6:30582600-30586400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:30582600-30586400	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr6:30582600-30586600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:30582600-30587000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:30583200-30586200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:30583600-30586600	Bivalent/Poised TSS	HepG2	liver
17	chr6:30583800-30586200	Active TSS	Spleen	Spleen
18	chr6:30584200-30586400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:30584200-30586400	Active TSS	Hela-S3	cervix
20	chr6:30584400-30586200	Active TSS	HUVEC	blood vessel
21	chr6:30584800-30586200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:30584800-30586200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:30584800-30586200	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr6:30584800-30586200	Active TSS	Fetal Muscle Trunk	muscle
25	chr6:30584800-30586200	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr6:30584800-30586200	Active TSS	Small Intestine	intestine
27	chr6:30584800-30586400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:30584800-30586400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:30584800-30586400	Active TSS	Brain Angular Gyrus	brain
30	chr6:30584800-30586400	Active TSS	Fetal Intestine Large	intestine
31	chr6:30584800-30586400	Active TSS	Fetal Kidney	kidney
32	chr6:30584800-30586400	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr6:30584800-30586600	Active TSS	H9 Cell Line	embryonic stem cell
34	chr6:30584800-30586600	Active TSS	Colonic Mucosa	Colon
35	chr6:30584800-30586600	Active TSS	Left Ventricle	heart
36	chr6:30584800-30586600	Active TSS	HSMM	muscle
37	chr6:30584800-30586800	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr6:30584800-30586800	Active TSS	Pancreas	Pancrea
39	chr6:30584800-30586800	Active TSS	NHDF-Ad	bronchial
40	chr6:30584800-30587000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:30584800-30587000	Active TSS	GM12878-XiMat	blood
42	chr6:30585000-30586200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:30585000-30586200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:30585000-30586200	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr6:30585000-30586200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:30585000-30586200	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr6:30585000-30586200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:30585000-30586200	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr6:30585000-30586200	Active TSS	Brain Cingulate Gyrus	brain
50	chr6:30585000-30586200	Active TSS	Pancreatic Islets	Pancreatic Islet

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