Variant report

Variant	rs2179368
Chromosome Location	chr6:149806552-149806553
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	YY1	chr6:149805685-149806604	HepG2	liver:	n/a	chr6:149806231-149806242 chr6:149806233-149806242
2	CHD2	chr6:149805813-149806929	GM12878	blood:	n/a	n/a
3	RELA	chr6:149805191-149806944	GM19193	blood:	n/a	n/a
4	STAT5A	chr6:149805628-149807090	GM12878	blood:	n/a	chr6:149806264-149806273
5	RELA	chr6:149805438-149806878	GM18526	blood:	n/a	n/a
6	HDAC2	chr6:149805743-149806887	HepG2	liver:	n/a	chr6:149806194-149806208 chr6:149806207-149806221 chr6:149806195-149806209 chr6:149806182-149806196 chr6:149806193-149806207 chr6:149806203-149806217 chr6:149806199-149806213 chr6:149806198-149806212
7	EP300	chr6:149805697-149806768	HepG2	liver:	n/a	chr6:149806198-149806212
8	CHD2	chr6:149805865-149806798	HepG2	liver:	n/a	n/a
9	RCOR1	chr6:149805120-149806914	GM12878	blood:	n/a	n/a
10	CEBPB	chr6:149805817-149807004	GM12878	blood:	n/a	n/a
11	NFATC1	chr6:149805895-149806750	GM12878	blood:	n/a	n/a
12	GATA3	chr6:149806399-149806680	T-47D	breast:	n/a	n/a
13	EP300	chr6:149805780-149806800	HepG2	liver:	n/a	chr6:149806198-149806212
14	MAX	chr6:149805837-149806593	ECC-1	luminal epithelium:	n/a	chr6:149806288-149806298 chr6:149806263-149806272
15	POLR2A	chr6:149806210-149806899	GM12891	blood:	n/a	n/a
16	EP300	chr6:149805754-149806961	GM12878	blood:	n/a	chr6:149806198-149806212
17	POLR2A	chr6:149801984-149806994	GM18951	blood:	n/a	n/a
18	RELA	chr6:149802797-149807059	GM12891	blood:	n/a	n/a
19	NFIC	chr6:149805736-149806831	HepG2	liver:	n/a	n/a
20	STAT1	chr6:149805863-149807021	GM12878	blood:	n/a	chr6:149806264-149806273
21	RAD21	chr6:149805884-149806974	GM12878	blood:	n/a	chr6:149806039-149806048
22	JUND	chr6:149805902-149806743	K562	blood:	n/a	chr6:149806262-149806273 chr6:149806260-149806271 chr6:149805943-149805951 chr6:149806361-149806375 chr6:149806262-149806274 chr6:149806264-149806273 chr6:149806262-149806269 chr6:149806263-149806274 chr6:149806233-149806242 chr6:149806263-149806273
23	SP1	chr6:149805816-149806870	GM12878	blood:	n/a	chr6:149806231-149806240 chr6:149806229-149806241 chr6:149806229-149806241 chr6:149806230-149806239 chr6:149806228-149806235
24	POU2F2	chr6:149805794-149806936	GM12891	blood:	n/a	n/a
25	POLR2A	chr6:149801790-149807098	GM12878	blood:	n/a	n/a
26	JUND	chr6:149805771-149806753	HepG2	liver:	n/a	chr6:149806262-149806273 chr6:149806260-149806271 chr6:149805943-149805951 chr6:149806361-149806375 chr6:149806262-149806274 chr6:149806264-149806273 chr6:149806262-149806269 chr6:149806263-149806274 chr6:149806233-149806242 chr6:149806263-149806273
27	MBD4	chr6:149805698-149807069	HepG2	liver:	n/a	n/a
28	FOSL2	chr6:149805767-149807033	HepG2	liver:	n/a	chr6:149806260-149806271 chr6:149805943-149805951 chr6:149806361-149806375 chr6:149806262-149806274 chr6:149806263-149806274 chr6:149806264-149806273 chr6:149806262-149806269 chr6:149806263-149806274 chr6:149806233-149806242 chr6:149806263-149806273
29	RUNX3	chr6:149805511-149807042	GM12878	blood:	n/a	n/a
30	TBP	chr6:149805486-149806863	GM12878	blood:	n/a	n/a
31	HNF4G	chr6:149805790-149806836	HepG2	liver:	n/a	chr6:149806274-149806286 chr6:149806273-149806286 chr6:149806399-149806407 chr6:149806273-149806286 chr6:149806271-149806286 chr6:149805886-149805894 chr6:149806274-149806286
32	WRNIP1	chr6:149805205-149807027	GM12878	blood:	n/a	n/a
33	MAFF	chr6:149805898-149806593	HepG2	liver:	n/a	n/a
34	FOXM1	chr6:149805703-149806948	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:149801932-149807132	GM12878	blood:	n/a	n/a
36	POLR2A	chr6:149806237-149806818	HepG2	liver:	n/a	n/a
37	POLR2A	chr6:149806004-149806589	HepG2	liver:	n/a	n/a
38	MXI1	chr6:149805763-149807035	HepG2	liver:	n/a	chr6:149806789-149806798
39	RELA	chr6:149805857-149806983	GM19099	blood:	n/a	n/a
40	YY1	chr6:149806433-149806837	GM12891	blood:	n/a	n/a
41	ZNF384	chr6:149805793-149806905	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:149805699-149806992	GM12892	blood:	n/a	n/a
43	RELA	chr6:149805528-149806938	GM12878	blood:	n/a	n/a
44	CTCF	chr6:149805631-149806931	GM12878	blood:	n/a	chr6:149806040-149806053
45	FOXM1	chr6:149805848-149807057	GM12878	blood:	n/a	n/a
46	SMC3	chr6:149805532-149806922	GM12878	blood:	n/a	chr6:149805947-149805955
47	POLR2A	chr6:149806304-149806656	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr6:149801889-149807107	Raji	blood:	n/a	n/a
49	IRF4	chr6:149806287-149806964	GM12878	blood:	n/a	n/a
50	MYBL2	chr6:149805646-149806783	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:149806502-149806552	HRE	kidney:	n/a
2	chr6:149806502-149806552	NB4	blood:	n/a
3	chr6:149806502-149806552	BJ	skin:	n/a
4	chr6:149806502-149806552	MCF10A-Er-Src	breast:	n/a
5	chr6:149806502-149806552	HCT-116	colon:	n/a
6	chr6:149806502-149806552	Hepatocyte	liver:	n/a
7	chr6:149806502-149806552	A549	lung:	n/a
8	chr6:149806502-149806552	HIPEpiC	eye:	n/a
9	chr6:149806502-149806552	AG09309	skin:	n/a
10	chr6:149806502-149806552	HCPEpiC	choroid plexus:	n/a
11	chr6:149806502-149806552	AG04449	skin:	fetal
12	chr6:149806502-149806552	SK-N-SH	brain:	n/a
13	chr6:149806502-149806552	NH-A	brain:	n/a
14	chr6:149806502-149806552	RPTEC	kidney:	n/a
15	chr6:149806502-149806552	SK-N-MC	brain:	n/a
16	chr6:149806502-149806552	ProgFib	skin:	n/a
17	chr6:149806502-149806552	IMR90	lung:	fetal
18	chr6:149806502-149806552	HUVEC	blood vessel:	n/a
19	chr6:149806502-149806552	GM19239	blood:	n/a
20	chr6:149806502-149806552	GM06990	blood:	n/a
21	chr6:149806502-149806552	LNCaP	prostate:	n/a
22	chr6:149806502-149806552	AG10803	skin:	n/a
23	chr6:149806502-149806552	CMK	blood:	n/a
24	chr6:149806502-149806552	AoSMC	blood vessel:	n/a
25	chr6:149806502-149806552	U87	brain:	n/a
26	chr6:149806502-149806552	HRCEpiC	kidney:	n/a
27	chr6:149806502-149806552	HRPEpiC	eye:	n/a
28	chr6:149806502-149806552	AG09319	gingival:	n/a
29	chr6:149806502-149806552	GM12891	blood:	n/a
30	chr6:149806502-149806552	SKMC	muscle:	n/a
31	chr6:149806502-149806552	T-47D	breast:	n/a
32	chr6:149806502-149806552	Hela-S3	cervix:	n/a
33	chr6:149806502-149806552	SAEC	small airway:	n/a
34	chr6:149806502-149806552	MCF-7	breast:	n/a
35	chr6:149806502-149806552	HepG2	liver:	n/a
36	chr6:149806502-149806552	AG04450	lung:	fetal
37	chr6:149806502-149806552	SK-N-SH_RA	brain:	n/a
38	chr6:149806502-149806552	NT2-D1	testis:	n/a
39	chr6:149806502-149806552	PrEC	prostate:	n/a
40	chr6:149806502-149806552	GM12892	blood:	n/a
41	chr6:149806502-149806552	HNPCEpiC	eye:	n/a
42	chr6:149806502-149806552	Caco-2	colon:	n/a
43	chr6:149806502-149806552	ovcar-3	ovarian:	n/a
44	chr6:149806502-149806552	PFSK-1	brain:	n/a
45	chr6:149806502-149806552	NHBE	bronchial:	n/a
46	chr6:149806502-149806552	PANC-1	pancreas:	n/a
47	chr6:149806502-149806552	HCF	heart:	n/a
48	chr6:149806502-149806552	GM12878	blood:	n/a
49	chr6:149806502-149806552	HAEpiC	amniotic membrane:	n/a
50	chr6:149806502-149806552	HEEpiC	esophagus:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149806502..149808230-chr6:149808327..149810146,3	MCF-7	breast:

Variant related genes	Relation type
ZC3H12D	TF binding region
ZC3H12D	CpG island

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2341768	0.81[CEU][hapmap]
rs2789504	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs4895791	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4897126	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4897127	0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv470866	chr6:149744632-149806552	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv1832313	chr6:149789511-149840750	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149801200-149807000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr6:149801600-149807200	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr6:149802200-149806800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr6:149802800-149806800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr6:149803800-149807000	Enhancers	Fetal Thymus	thymus
6	chr6:149803800-149807000	Enhancers	Left Ventricle	heart
7	chr6:149804200-149806600	Weak transcription	Pancreas	Pancrea
8	chr6:149804400-149824600	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:149804600-149807000	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr6:149804600-149807400	Enhancers	Primary hematopoietic stem cells	blood
11	chr6:149805000-149806800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr6:149805000-149807000	Active TSS	Rectal Smooth Muscle	rectum
13	chr6:149805000-149807200	Flanking Active TSS	GM12878-XiMat	blood
14	chr6:149805000-149807400	Enhancers	Small Intestine	intestine
15	chr6:149805200-149807000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:149805600-149806600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:149805800-149806600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:149805800-149806800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:149805800-149806800	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr6:149805800-149806800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:149805800-149806800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr6:149805800-149806800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:149805800-149806800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:149805800-149806800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:149805800-149806800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:149805800-149806800	Enhancers	Esophagus	oesophagus
27	chr6:149805800-149806800	Enhancers	Right Ventricle	heart
28	chr6:149805800-149806800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr6:149805800-149806800	Enhancers	NHDF-Ad	bronchial
30	chr6:149805800-149807000	Enhancers	Placenta	Placenta
31	chr6:149805800-149807000	Enhancers	Lung	lung
32	chr6:149805800-149807000	Enhancers	Psoas Muscle	Psoas
33	chr6:149805800-149807000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr6:149805800-149807000	Flanking Active TSS	Dnd41	blood
35	chr6:149806000-149806600	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr6:149806000-149806600	Flanking Active TSS	Thymus	Thymus
37	chr6:149806000-149806600	Enhancers	Hela-S3	cervix
38	chr6:149806000-149806600	Enhancers	NH-A	brain
39	chr6:149806000-149806800	Enhancers	H1 Cell Line	embryonic stem cell
40	chr6:149806000-149806800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:149806000-149806800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:149806000-149806800	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr6:149806000-149806800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr6:149806000-149806800	Enhancers	Fetal Lung	lung
45	chr6:149806000-149806800	Enhancers	HSMM	muscle
46	chr6:149806000-149806800	Bivalent Enhancer	K562	blood
47	chr6:149806000-149807000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr6:149806200-149806600	Enhancers	Primary T cells from cord blood	blood
49	chr6:149806200-149806800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr6:149806200-149807000	Flanking Active TSS	Primary B cells from peripheral blood	blood

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