Variant report

Variant	rs566086431
Chromosome Location	chr6:33378496-33378497
allele	C/G
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	RUNX3	chr6:33377614-33378701	GM12878	blood:	n/a	n/a
2	E2F6	chr6:33377655-33378509	A549	lung:	n/a	n/a
3	POLR2A	chr6:33377703-33378699	A549	lung:	n/a	n/a
4	ESRRA	chr6:33377416-33379769	GM12878	blood:	n/a	chr6:33378216-33378229 chr6:33378393-33378411 chr6:33379217-33379227 chr6:33379217-33379226 chr6:33379195-33379214 chr6:33377801-33377813
5	SP1	chr6:33378453-33378718	GM12878	blood:	n/a	chr6:33378456-33378466 chr6:33378457-33378466 chr6:33378456-33378466 chr6:33378456-33378465
6	POLR2A	chr6:33377702-33379363	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr6:33377525-33379636	H1-hESC	embryonic stem cell:	n/a	n/a
8	CREB1	chr6:33377589-33378593	K562	blood:	n/a	chr6:33378124-33378137
9	POLR2A	chr6:33378421-33379179	GM12892	blood:	n/a	n/a
10	POLR2A	chr6:33377198-33378902	HL-60	blood:	n/a	n/a
11	SP1	chr6:33377573-33378941	HCT-116	colon:	n/a	chr6:33378405-33378414 chr6:33378456-33378466 chr6:33378406-33378415 chr6:33378098-33378119 chr6:33378348-33378360 chr6:33378323-33378333 chr6:33378405-33378415 chr6:33378431-33378440 chr6:33378006-33378015 chr6:33378457-33378466 chr6:33378456-33378466 chr6:33378349-33378358 chr6:33378004-33378016 chr6:33378052-33378066 chr6:33378255-33378269 chr6:33378322-33378334 chr6:33378404-33378416 chr6:33378180-33378192 chr6:33378349-33378359 chr6:33377739-33377753 chr6:33378430-33378442 chr6:33378456-33378465 chr6:33378371-33378381 chr6:33378427-33378441 chr6:33378180-33378192 chr6:33378345-33378359 chr6:33377883-33377893 chr6:33378004-33378015 chr6:33378404-33378416 chr6:33378350-33378359 chr6:33378323-33378333 chr6:33378432-33378441 chr6:33378348-33378360 chr6:33378182-33378191 chr6:33378051-33378062 chr6:33378430-33378442
12	CHD2	chr6:33377866-33378624	H1-hESC	embryonic stem cell:	n/a	chr6:33378144-33378154
13	ZBTB7A	chr6:33378378-33378675	HepG2	liver:	n/a	n/a
14	MAX	chr6:33377876-33378787	SK-N-SH	brain:	n/a	chr6:33378349-33378359 chr6:33378405-33378415
15	MAX	chr6:33377852-33378750	H1-hESC	embryonic stem cell:	n/a	chr6:33378349-33378359 chr6:33378405-33378415
16	E2F4	chr6:33377756-33379148	K562	blood:	n/a	chr6:33378144-33378155
17	POLR2A	chr6:33376663-33380029	HepG2	liver:	n/a	n/a
18	MAX	chr6:33377583-33378588	A549	lung:	n/a	chr6:33378349-33378359 chr6:33378405-33378415
19	REST	chr6:33377527-33379367	H1-neurons	neurons:	n/a	chr6:33378320-33378333
20	POLR2A	chr6:33378441-33378682	H1-hESC	embryonic stem cell:	n/a	n/a
21	FOXM1	chr6:33377747-33378508	MCF-7	breast:	n/a	n/a
22	POLR2A	chr6:33377167-33378995	K562	blood:	n/a	n/a
23	POLR2A	chr6:33376768-33379235	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr6:33378437-33378728	SK-N-SH	brain:	n/a	n/a
25	USF1	chr6:33378072-33378522	SK-N-SH_RA	brain:	n/a	n/a
26	POLR2A	chr6:33377277-33378886	HL-60	blood:	n/a	n/a
27	POLR2A	chr6:33376964-33379018	K562	blood:	n/a	n/a
28	POLR2A	chr6:33377397-33379021	Raji	blood:	n/a	n/a
29	TAF1	chr6:33378414-33378690	H1-hESC	embryonic stem cell:	n/a	n/a
30	SIN3AK20	chr6:33378433-33378683	HepG2	liver:	n/a	n/a
31	MYC	chr6:33378458-33378515	HUVEC	blood vessel:	n/a	n/a
32	EBF1	chr6:33378440-33378665	GM12878	blood:	n/a	chr6:33378536-33378547
33	CBX3	chr6:33377136-33378708	K562	blood:	n/a	n/a
34	PAX5	chr6:33378429-33378839	GM12878	blood:	n/a	n/a
35	IRF1	chr6:33377757-33378983	K562	blood:	n/a	chr6:33378430-33378444 chr6:33377880-33377894 chr6:33378180-33378194 chr6:33378049-33378063 chr6:33378004-33378018 chr6:33378404-33378418 chr6:33378348-33378362 chr6:33378109-33378118
36	POLR2A	chr6:33377729-33379203	H1-neurons	neurons:	n/a	n/a
37	RELA	chr6:33377779-33378743	GM19193	blood:	n/a	n/a
38	TCF12	chr6:33377604-33378833	A549	lung:	n/a	n/a
39	POLR2A	chr6:33377681-33379306	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:33377829-33379042	GM10847	blood:	n/a	n/a
41	CREB1	chr6:33377662-33378701	GM12878	blood:	n/a	chr6:33378124-33378137
42	RCOR1	chr6:33377726-33378594	Hela-S3	cervix:	n/a	n/a
43	GATA3	chr6:33377750-33378511	MCF-7	breast:	n/a	n/a
44	MAX	chr6:33377721-33379073	K562	blood:	n/a	chr6:33378349-33378359 chr6:33378405-33378415
45	SP1	chr6:33377659-33378575	A549	lung:	n/a	chr6:33378405-33378414 chr6:33378456-33378466 chr6:33378406-33378415 chr6:33378098-33378119 chr6:33378348-33378360 chr6:33378323-33378333 chr6:33378405-33378415 chr6:33378431-33378440 chr6:33378006-33378015 chr6:33378457-33378466 chr6:33378456-33378466 chr6:33378349-33378358 chr6:33378004-33378016 chr6:33378052-33378066 chr6:33378255-33378269 chr6:33378322-33378334 chr6:33378404-33378416 chr6:33378180-33378192 chr6:33378349-33378359 chr6:33377739-33377753 chr6:33378430-33378442 chr6:33378456-33378465 chr6:33378371-33378381 chr6:33378427-33378441 chr6:33378180-33378192 chr6:33378345-33378359 chr6:33377883-33377893 chr6:33378004-33378015 chr6:33378404-33378416 chr6:33378350-33378359 chr6:33378323-33378333 chr6:33378432-33378441 chr6:33378348-33378360 chr6:33378182-33378191 chr6:33378051-33378062 chr6:33378430-33378442
46	PBX3	chr6:33377692-33378725	A549	lung:	n/a	chr6:33378108-33378117
47	POLR2A	chr6:33378442-33378701	A549	lung:	n/a	n/a
48	SIN3AK20	chr6:33377778-33378673	PFSK-1	brain:	n/a	n/a
49	PML	chr6:33377149-33378856	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:33378417-33379440	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33279489..33293095-chr6:33375317..33398824,56	K562	blood:
2	chr6:32938764..32940269-chr6:33377609..33379519,2	MCF-7	breast:
3	chr6:33377039..33379614-chr6:33421781..33424452,2	K562	blood:
4	chr6:33167104..33169096-chr6:33376083..33378504,2	K562	blood:
5	chr17:75283611..75284123-chr6:33378111..33378909,2	Hela-S3	cervix:
6	chr16:25268976..25269623-chr6:33377932..33378898,2	Hela-S3	cervix:
7	chr1:28974856..28975665-chr6:33378255..33378960,2	Hela-S3	cervix:
8	chr6:33377496..33379251-chr6:33661661..33664420,2	MCF-7	breast:
9	chr6:33261265..33262842-chr6:33377823..33379768,2	K562	blood:
10	chr6:33237157..33241221-chr6:33375922..33380109,6	MCF-7	breast:
11	chr6:33357351..33361150-chr6:33373102..33380127,12	MCF-7	breast:
12	chr6:27114748..27115280-chr6:33378038..33378746,2	Hela-S3	cervix:
13	chr12:52444856..52445551-chr6:33378224..33378869,2	Hela-S3	cervix:
14	chr6:33256522..33259302-chr6:33375799..33380992,5	MCF-7	breast:
15	chr6:30710804..30712449-chr6:33376908..33379450,2	MCF-7	breast:
16	chr6:33255490..33258967-chr6:33375507..33378634,5	MCF-7	breast:
17	chr6:33237328..33248026-chr6:33370896..33379989,29	K562	blood:
18	chr6:33166881..33169550-chr6:33376292..33379063,3	K562	blood:
19	chr6:33215707..33217514-chr6:33377026..33379165,2	K562	blood:
20	chr6:33358222..33360525-chr6:33377821..33380717,3	MCF-7	breast:
21	chr6:33280795..33292485-chr6:33374786..33387605,31	K562	blood:
22	chr6:33280452..33282497-chr6:33377188..33378997,2	MCF-7	breast:
23	chr6:33255152..33256710-chr6:33377924..33379590,2	K562	blood:
24	chr6:33263073..33268205-chr6:33376944..33380191,7	MCF-7	breast:
25	chr6:33261342..33263204-chr6:33376924..33379323,2	K562	blood:
26	chr6:33237079..33247876-chr6:33369927..33381738,26	K562	blood:
27	chr6:33356271..33363521-chr6:33371085..33380351,32	K562	blood:
28	chr6:33244680..33251060-chr6:33375427..33382644,12	MCF-7	breast:
29	chr10:134145639..134146221-chr6:33378370..33378986,2	Hela-S3	cervix:
30	chr6:33242863..33248981-chr6:33374531..33379553,10	MCF-7	breast:

Variant related genes	Relation type
PHF1	TF binding region
ENSG00000223501	Chromatin interaction
ENSG00000235863	Chromatin interaction
ENSG00000155592	Chromatin interaction
ENSG00000237441	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000204220	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000204231	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000148814	Chromatin interaction
ENSG00000232940	Chromatin interaction
ENSG00000225644	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000112473	Chromatin interaction
ENSG00000184640	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000202441	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000269490	Chromatin interaction
ENSG00000204209	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

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	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	esv3439586	chr6:33376999-33380347	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	29 gene(s)	inside rSNPs	diseases
4	esv3335292	chr6:33377349-33379972	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
5	nsv885769	chr6:33377522-33412197	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers 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 miRNA	48 gene(s)	inside rSNPs	diseases
6	esv3354637	chr6:33377724-33379522	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 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	chr6:33376600-33380000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:33377000-33379600	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:33377200-33379200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:33377200-33379200	Active TSS	Colonic Mucosa	Colon
5	chr6:33377200-33379400	Active TSS	Rectal Smooth Muscle	rectum
6	chr6:33377200-33379600	Active TSS	H9 Cell Line	embryonic stem cell
7	chr6:33377200-33379600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:33377200-33379800	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr6:33377200-33379800	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr6:33377200-33380000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:33377400-33379000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:33377400-33379200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:33377400-33379400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr6:33377400-33379400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:33377400-33379400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:33377400-33379400	Active TSS	Fetal Brain Female	brain
17	chr6:33377400-33379400	Active TSS	A549	lung
18	chr6:33377400-33379600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr6:33377400-33379600	Active TSS	Brain Substantia Nigra	brain
20	chr6:33377400-33379800	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr6:33377400-33379800	Active TSS	Right Ventricle	heart
22	chr6:33377600-33379200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:33377600-33379400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:33377600-33379400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:33377600-33379400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:33377600-33379400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:33377600-33379400	Active TSS	Duodenum Mucosa	Duodenum
28	chr6:33377600-33379400	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr6:33377600-33379400	Active TSS	Lung	lung
30	chr6:33377600-33379600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:33377600-33379600	Active TSS	Esophagus	oesophagus
32	chr6:33377600-33379600	Active TSS	Fetal Kidney	kidney
33	chr6:33377600-33379600	Active TSS	Left Ventricle	heart
34	chr6:33377600-33379600	Active TSS	Placenta Amnion	Placenta Amnion
35	chr6:33377600-33379600	Active TSS	HSMMtube	muscle
36	chr6:33377600-33379800	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr6:33377600-33379800	Active TSS	Ovary	ovary
38	chr6:33377600-33379800	Active TSS	Psoas Muscle	Psoas
39	chr6:33377600-33380000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:33377600-33380000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:33377600-33380000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:33377600-33380000	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr6:33377800-33379000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr6:33377800-33379000	Active TSS	Monocytes-CD14+_RO01746	blood
45	chr6:33377800-33379200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:33377800-33379200	Active TSS	Primary monocytes fromperipheralblood	blood
47	chr6:33377800-33379200	Active TSS	Primary T cells from cord blood	blood
48	chr6:33377800-33379200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr6:33377800-33379200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:33377800-33379200	Active TSS	Adipose Nuclei	Adipose

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