Variant report

Variant	rs9397451
Chromosome Location	chr6:150244261-150244262
allele	A/C
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	TCF7L2	chr6:150244183-150244505	Hela-S3	cervix:	n/a	n/a
2	SIN3A	chr6:150243787-150244660	H1-hESC	embryonic stem cell:	n/a	chr6:150243944-150243957 chr6:150243804-150243815
3	MAZ	chr6:150243565-150244775	IMR90	lung:	n/a	chr6:150244690-150244700
4	SP1	chr6:150243951-150244604	H1-hESC	embryonic stem cell:	n/a	chr6:150244284-150244293 chr6:150244283-150244295 chr6:150244284-150244294 chr6:150244285-150244294 chr6:150244026-150244038 chr6:150244283-150244294 chr6:150244284-150244293 chr6:150244284-150244294 chr6:150244283-150244295
5	POLR2A	chr6:150243996-150244507	HUVEC	blood vessel:	n/a	n/a
6	RAD21	chr6:150243788-150244711	IMR90	lung:	n/a	chr6:150244161-150244171 chr6:150243810-150243822 chr6:150243811-150243824
7	NFYA	chr6:150244168-150244554	Hela-S3	cervix:	n/a	chr6:150244324-150244342 chr6:150244324-150244339 chr6:150244324-150244338 chr6:150244324-150244339 chr6:150244326-150244336 chr6:150244326-150244336 chr6:150244324-150244337
8	CHD2	chr6:150243790-150244550	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr6:150243933-150244529	MCF-7	breast:	n/a	n/a
10	POLR2A	chr6:150243999-150244620	U87	brain:	n/a	n/a
11	RAD21	chr6:150244094-150244497	Hela-S3	cervix:	n/a	chr6:150244161-150244171
12	POLR2A	chr6:150243941-150244497	MCF-7	breast:	n/a	n/a
13	E2F6	chr6:150244055-150244819	H1-hESC	embryonic stem cell:	n/a	chr6:150244326-150244335
14	POLR2A	chr6:150243999-150244575	U87	brain:	n/a	n/a
15	TCF7L2	chr6:150244065-150244500	PANC-1	pancreas:	n/a	n/a
16	TAF1	chr6:150244038-150244547	H1-hESC	embryonic stem cell:	n/a	n/a
17	MXI1	chr6:150243884-150244863	SK-N-SH	brain:	n/a	n/a
18	MYC	chr6:150244186-150244505	MCF10A-Er-Src	breast:	n/a	n/a
19	SP4	chr6:150244105-150244576	H1-hESC	embryonic stem cell:	n/a	chr6:150244283-150244294
20	SPI1	chr6:150244140-150244592	HL-60	blood:	n/a	chr6:150244396-150244409
21	POLR2A	chr6:150243942-150244433	MCF10A-Er-Src	breast:	n/a	n/a
22	MAX	chr6:150243989-150244738	H1-hESC	embryonic stem cell:	n/a	chr6:150244690-150244700
23	NFYB	chr6:150244203-150244473	GM12878	blood:	n/a	chr6:150244324-150244339 chr6:150244324-150244338 chr6:150244324-150244339 chr6:150244326-150244336 chr6:150244326-150244336 chr6:150244324-150244337 chr6:150244321-150244336
24	POLR2A	chr6:150243961-150244465	HUVEC	blood vessel:	n/a	n/a
25	YY1	chr6:150243919-150244282	HepG2	liver:	n/a	n/a
26	RCOR1	chr6:150244152-150244447	Hela-S3	cervix:	n/a	n/a
27	CEBPB	chr6:150244184-150244557	H1-hESC	embryonic stem cell:	n/a	chr6:150244327-150244335
28	USF2	chr6:150244180-150244585	H1-hESC	embryonic stem cell:	n/a	n/a
29	FOS	chr6:150244258-150244567	MCF10A-Er-Src	breast:	n/a	chr6:150244328-150244337
30	TAF1	chr6:150244024-150244613	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr6:150244090-150244346	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr6:150244036-150244353	ProgFib	skin:	n/a	n/a
33	NFIC	chr6:150244039-150244858	ECC-1	luminal epithelium:	n/a	n/a
34	HCFC1	chr6:150244260-150244286	K562	blood:	n/a	n/a
35	MAX	chr6:150244196-150244459	A549	lung:	n/a	n/a
36	POLR2A	chr6:150244022-150244461	ECC-1	luminal epithelium:	n/a	n/a
37	MAX	chr6:150243935-150244853	ECC-1	luminal epithelium:	n/a	chr6:150244690-150244700
38	KAP1	chr6:150244140-150244547	U2OS	brain:	n/a	chr6:150244336-150244344
39	MYC	chr6:150244223-150244522	MCF10A-Er-Src	breast:	n/a	n/a
40	MXI1	chr6:150243746-150244842	IMR90	lung:	n/a	n/a
41	CTCF	chr6:150244120-150244270	WERI-Rb-1	eye:	n/a	n/a
42	MXI1	chr6:150244050-150244443	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr6:150244062-150244491	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr6:150244091-150244262	A549	lung:	n/a	n/a
45	NFYB	chr6:150244146-150244511	K562	blood:	n/a	chr6:150244324-150244339 chr6:150244324-150244338 chr6:150244324-150244339 chr6:150244326-150244336 chr6:150244326-150244336 chr6:150244324-150244337 chr6:150244321-150244336
46	NFYB	chr6:150244148-150244511	Hela-S3	cervix:	n/a	chr6:150244324-150244339 chr6:150244324-150244338 chr6:150244324-150244339 chr6:150244326-150244336 chr6:150244326-150244336 chr6:150244324-150244337 chr6:150244321-150244336
47	E2F4	chr6:150244180-150244490	MCF10A-Er-Src	breast:	n/a	chr6:150244326-150244335
48	SIN3AK20	chr6:150243802-150244429	PANC-1	pancreas:	n/a	n/a
49	RCOR1	chr6:150244218-150244434	K562	blood:	n/a	n/a
50	POLR2A	chr6:150243998-150244379	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:149865589..149867401-chr6:150242514..150245357,2	MCF-7	breast:
2	chr6:150217021..150219534-chr6:150242538..150245487,2	MCF-7	breast:
3	chr6:150181490..150187274-chr6:150243970..150248410,8	MCF-7	breast:

Variant related genes	Relation type
RAET1G	TF binding region
ENSG00000164520	Chromatin interaction
ENSG00000268592	Chromatin interaction
ENSG00000131013	Chromatin interaction
ENSG00000120256	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10457853	0.93[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17079029	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2342773	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4142628	0.87[CEU][hapmap];0.83[CHB][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6557137	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs6557163	0.88[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6904335	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6905778	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6910351	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6915465	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6927913	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6936944	0.88[CEU][hapmap];0.87[CHB][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72997594	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7745070	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7761734	0.93[EUR][1000 genomes]
rs9322226	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs9322227	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs9322230	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9322231	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9371216	0.86[EUR][1000 genomes]
rs9371523	0.87[EUR][1000 genomes]
rs9371539	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs9371555	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9383569	0.86[EUR][1000 genomes]
rs9383573	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs9383583	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs9383916	0.88[EUR][1000 genomes]
rs9383942	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9383943	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9383944	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9383945	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9397049	0.86[EUR][1000 genomes]
rs9397053	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs9397056	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs9397057	0.88[EUR][1000 genomes]
rs9397060	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs9397071	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9397394	0.85[EUR][1000 genomes]
rs9397399	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9397419	0.88[EUR][1000 genomes]
rs9397447	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9397449	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv970172	chr6:150235248-150244455	Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150242800-150247800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:150243400-150244400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
3	chr6:150243400-150244400	Active TSS	Hela-S3	cervix
4	chr6:150243400-150244800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:150243400-150244800	Flanking Active TSS	HMEC	breast
6	chr6:150243400-150245000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr6:150243400-150245000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:150243600-150244400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
9	chr6:150243600-150244400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:150243600-150244400	Active TSS	Muscle Satellite Cultured Cells	--
11	chr6:150243600-150244400	Bivalent Enhancer	Fetal Brain Male	brain
12	chr6:150243600-150244400	Active TSS	Fetal Lung	lung
13	chr6:150243600-150244400	Active TSS	NHEK	skin
14	chr6:150243600-150244600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:150243600-150244600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:150243600-150244600	Active TSS	A549	lung
17	chr6:150243600-150244600	Active TSS	NHDF-Ad	bronchial
18	chr6:150243600-150244800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
19	chr6:150243600-150244800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr6:150243600-150244800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr6:150243600-150244800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr6:150243600-150244800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:150243600-150244800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
24	chr6:150243600-150244800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
25	chr6:150243600-150244800	Flanking Bivalent TSS/Enh	HepG2	liver
26	chr6:150243600-150244800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
27	chr6:150243600-150245000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:150243600-150245000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:150243600-150245000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:150243800-150244400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:150243800-150244400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:150243800-150244400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:150243800-150244400	Bivalent Enhancer	Fetal Thymus	thymus
34	chr6:150243800-150244400	Active TSS	HSMM	muscle
35	chr6:150243800-150244400	Active TSS	Osteobl	bone
36	chr6:150243800-150244600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
37	chr6:150243800-150244600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:150243800-150244600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:150243800-150244600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:150243800-150244600	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr6:150243800-150244600	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr6:150243800-150244600	Active TSS	Gastric	stomach
43	chr6:150243800-150244600	Bivalent/Poised TSS	Psoas Muscle	Psoas
44	chr6:150243800-150244600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr6:150243800-150244600	Active TSS	NHLF	lung
46	chr6:150243800-150244800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
47	chr6:150243800-150244800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:150243800-150244800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
49	chr6:150243800-150244800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
50	chr6:150243800-150244800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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