Variant report

Variant	rs1342331
Chromosome Location	chr6:144066159-144066160
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	POLR2A	chr6:144065960-144068161	HepG2	liver:	n/a	n/a
2	FOSL2	chr6:144065570-144067163	HepG2	liver:	n/a	chr6:144065839-144065848 chr6:144066135-144066142 chr6:144065864-144065872 chr6:144066865-144066874 chr6:144066134-144066143 chr6:144066134-144066142
3	GATA3	chr6:144065877-144067046	MCF-7	breast:	n/a	chr6:144066001-144066017
4	SMC3	chr6:144065982-144067741	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:144065560-144069107	HepG2	liver:	n/a	n/a
6	JUN	chr6:144065981-144067112	HepG2	liver:	n/a	chr6:144066135-144066142 chr6:144066865-144066874 chr6:144066134-144066143 chr6:144066134-144066142
7	GATA3	chr6:144065849-144067154	A549	lung:	n/a	chr6:144066001-144066017
8	RFX5	chr6:144066132-144067080	HepG2	liver:	n/a	chr6:144066866-144066875 chr6:144066823-144066832 chr6:144066820-144066835
9	FOSL1	chr6:144065845-144066418	HCT-116	colon:	n/a	chr6:144066135-144066142 chr6:144065864-144065872 chr6:144066134-144066143 chr6:144066134-144066142
10	FOXA1	chr6:144065875-144067262	HepG2	liver:	n/a	chr6:144066720-144066735 chr6:144066739-144066754
11	USF2	chr6:144066124-144066601	HepG2	liver:	n/a	n/a
12	HEY1	chr6:144066111-144067271	HepG2	liver:	n/a	n/a
13	FOXA2	chr6:144065994-144066296	A549	lung:	n/a	n/a
14	FOXA1	chr6:144065753-144067250	HepG2	liver:	n/a	chr6:144066720-144066735 chr6:144066739-144066754
15	MYBL2	chr6:144065411-144067275	HepG2	liver:	n/a	n/a
16	RXRA	chr6:144065991-144067155	HepG2	liver:	n/a	chr6:144066134-144066143 chr6:144066133-144066142 chr6:144066214-144066228
17	FOS	chr6:144066008-144066293	MCF10A-Er-Src	breast:	n/a	chr6:144066135-144066142 chr6:144066134-144066143 chr6:144066134-144066142
18	RCOR1	chr6:144066101-144066198	K562	blood:	n/a	n/a
19	BHLHE40	chr6:144065690-144067663	HepG2	liver:	n/a	n/a
20	HDAC2	chr6:144065861-144066985	MCF-7	breast:	n/a	chr6:144066144-144066153
21	FOSL2	chr6:144065778-144066382	HepG2	liver:	n/a	chr6:144065839-144065848 chr6:144066135-144066142 chr6:144065864-144065872 chr6:144066134-144066143 chr6:144066134-144066142
22	FOSL2	chr6:144065869-144066399	MCF-7	breast:	n/a	chr6:144066135-144066142 chr6:144066134-144066143 chr6:144066134-144066142
23	EP300	chr6:144065949-144066396	HepG2	liver:	n/a	chr6:144066048-144066062 chr6:144066134-144066143 chr6:144066133-144066142
24	FOXA2	chr6:144065906-144067202	HepG2	liver:	n/a	n/a
25	KAP1	chr6:144065821-144067450	U2OS	brain:	n/a	chr6:144066135-144066144
26	POLR2A	chr6:144066103-144067132	HepG2	liver:	n/a	n/a
27	HEY1	chr6:144065698-144067968	HepG2	liver:	n/a	chr6:144065832-144065841
28	MBD4	chr6:144065846-144067368	HepG2	liver:	n/a	n/a
29	TCF7L2	chr6:144065916-144066326	MCF-7	breast:	n/a	chr6:144066134-144066143
30	KAP1	chr6:144064616-144067815	HEK293	kidney:	n/a	chr6:144066135-144066144
31	FOS	chr6:144065968-144066292	MCF10A-Er-Src	breast:	n/a	chr6:144066135-144066142 chr6:144066134-144066143 chr6:144066134-144066142
32	ARID3A	chr6:144065690-144067812	HepG2	liver:	n/a	n/a
33	JUND	chr6:144065942-144067197	HepG2	liver:	n/a	chr6:144066132-144066143 chr6:144066135-144066142 chr6:144066865-144066874 chr6:144066134-144066143 chr6:144066134-144066142
34	POLR2A	chr6:144066092-144067937	HepG2	liver:	n/a	n/a
35	TBP	chr6:144066028-144067959	HepG2	liver:	n/a	n/a
36	POLR2A	chr6:144066100-144067261	PANC-1	pancreas:	n/a	n/a
37	TEAD4	chr6:144065865-144067979	HepG2	liver:	n/a	n/a
38	SP1	chr6:144066123-144067230	A549	lung:	n/a	chr6:144066856-144066877
39	JUND	chr6:144066052-144066252	K562	blood:	n/a	chr6:144066132-144066143 chr6:144066135-144066142 chr6:144066134-144066143 chr6:144066134-144066142
40	EP300	chr6:144066119-144068178	ECC-1	luminal epithelium:	n/a	chr6:144066134-144066143 chr6:144066133-144066142
41	JUND	chr6:144065834-144066388	HCT-116	colon:	n/a	chr6:144066132-144066143 chr6:144065839-144065848 chr6:144066135-144066142 chr6:144065864-144065872 chr6:144066134-144066143 chr6:144066134-144066142
42	FOSL2	chr6:144066041-144066243	A549	lung:	n/a	chr6:144066135-144066142 chr6:144066134-144066143 chr6:144066134-144066142
43	GATA3	chr6:144065869-144067245	MCF-7	breast:	n/a	chr6:144066001-144066017
44	RXRA	chr6:144065998-144067086	HepG2	liver:	n/a	chr6:144066134-144066143 chr6:144066133-144066142 chr6:144066214-144066228
45	FOXA1	chr6:144065854-144067228	HepG2	liver:	n/a	chr6:144066720-144066735 chr6:144066739-144066754
46	RCOR1	chr6:144066136-144067463	HepG2	liver:	n/a	n/a
47	HNF4G	chr6:144066041-144067095	HepG2	liver:	n/a	n/a
48	FOS	chr6:144066027-144066301	MCF10A-Er-Src	breast:	n/a	chr6:144066135-144066142 chr6:144066134-144066143 chr6:144066134-144066142
49	JUND	chr6:144065956-144066303	HepG2	liver:	n/a	chr6:144066132-144066143 chr6:144066135-144066142 chr6:144066134-144066143 chr6:144066134-144066142
50	HDAC2	chr6:144066005-144067266	HepG2	liver:	n/a	chr6:144066144-144066153

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:143998734..144000526-chr6:144065898..144068139,2	MCF-7	breast:
2	chr6:144064761..144067514-chr6:144068407..144072596,5	MCF-7	breast:

Variant related genes	Relation type
PHACTR2	TF binding region
ENSG00000112419	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10484829	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11155321	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11155323	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11752220	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11962678	0.96[CEU][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs12197846	0.96[CEU][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes]
rs12207527	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12208670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216126	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17521652	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1935497	0.96[CEU][hapmap];0.99[EUR][1000 genomes]
rs2235995	0.85[CEU][hapmap];0.82[CHB][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2273211	0.96[CEU][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs2281405	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3818113	1.00[ASW][hapmap];0.96[CEU][hapmap];0.88[GIH][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55935224	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59307773	0.85[ASN][1000 genomes]
rs72556977	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72556986	0.97[EUR][1000 genomes]
rs736784	1.00[ASW][hapmap];0.84[CEU][hapmap];0.87[GIH][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs736785	0.96[CEU][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7738780	0.94[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144038600-144075400	Weak transcription	NHEK	skin
2	chr6:144046200-144074600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr6:144053400-144076600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:144053600-144073600	Weak transcription	Osteobl	bone
5	chr6:144053600-144075400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr6:144053600-144075600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr6:144053800-144079800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:144056000-144067600	Weak transcription	K562	blood
9	chr6:144056200-144080200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:144059800-144077000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:144060000-144066400	Weak transcription	Fetal Brain Female	brain
12	chr6:144060200-144078400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:144060600-144074600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr6:144060800-144074400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:144061000-144079800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr6:144061000-144086600	Weak transcription	Primary T cells from cord blood	blood
17	chr6:144062800-144066400	Enhancers	Stomach Mucosa	stomach
18	chr6:144063000-144075400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:144063200-144066200	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr6:144063400-144066400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr6:144063400-144066400	Enhancers	Fetal Stomach	stomach
22	chr6:144063400-144066600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr6:144063400-144066800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:144063400-144067200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr6:144063400-144067800	Enhancers	Lung	lung
26	chr6:144063400-144068000	Enhancers	Psoas Muscle	Psoas
27	chr6:144063400-144069000	Enhancers	Left Ventricle	heart
28	chr6:144063400-144069200	Enhancers	Fetal Heart	heart
29	chr6:144063400-144070600	Enhancers	H9 Cell Line	embryonic stem cell
30	chr6:144063400-144071400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:144063600-144066200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr6:144063600-144066200	Enhancers	Pancreas	Pancrea
33	chr6:144063600-144066400	Enhancers	Small Intestine	intestine
34	chr6:144063600-144066600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:144063600-144066800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:144063600-144067400	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr6:144063600-144068800	Enhancers	Right Ventricle	heart
38	chr6:144063600-144069000	Enhancers	Placenta Amnion	Placenta Amnion
39	chr6:144063600-144076600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:144063800-144066200	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr6:144063800-144066200	Enhancers	Fetal Intestine Small	intestine
42	chr6:144063800-144066400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr6:144063800-144066600	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr6:144063800-144068000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr6:144063800-144075000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:144063800-144086400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:144064000-144066400	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr6:144064000-144066400	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr6:144064000-144067200	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr6:144064200-144066200	Enhancers	Pancreatic Islets	Pancreatic Islet

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