Variant report

Variant	rs7746456
Chromosome Location	chr6:73330069-73330070
allele	A/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	MTA3	chr6:73329476-73330787	GM12878	blood:	n/a	n/a
2	NRF1	chr6:73329775-73330150	GM12878	blood:	n/a	n/a
3	SP1	chr6:73329582-73330263	GM12878	blood:	n/a	chr6:73329903-73329915 chr6:73329904-73329918 chr6:73329903-73329915 chr6:73330160-73330174 chr6:73329905-73329914
4	CTCF	chr6:73329766-73330069	K562	blood:	n/a	n/a
5	EGR1	chr6:73329762-73330422	GM12878	blood:	n/a	chr6:73330028-73330041 chr6:73329907-73329917 chr6:73330302-73330311 chr6:73330028-73330041 chr6:73330029-73330040 chr6:73330300-73330311 chr6:73330030-73330039 chr6:73329905-73329920 chr6:73330029-73330040 chr6:73330024-73330046 chr6:73330031-73330040 chr6:73330299-73330313 chr6:73330027-73330042 chr6:73329906-73329919 chr6:73330028-73330042 chr6:73330030-73330040 chr6:73330028-73330041 chr6:73330030-73330040
6	FOXM1	chr6:73329583-73330299	GM12878	blood:	n/a	n/a
7	CTCF	chr6:73330020-73330170	AG04449	skin:	n/a	n/a
8	POLR2A	chr6:73329851-73330238	K562	blood:	n/a	n/a
9	BATF	chr6:73329611-73330220	GM12878	blood:	n/a	n/a
10	NFIC	chr6:73329489-73330315	GM12878	blood:	n/a	n/a
11	EP300	chr6:73329606-73330483	GM12878	blood:	n/a	chr6:73329750-73329759
12	POLR2A	chr6:73329493-73333253	NB4	blood:	n/a	n/a
13	STAT5A	chr6:73329719-73330154	GM12878	blood:	n/a	chr6:73329901-73329913
14	USF1	chr6:73329959-73330217	GM12878	blood:	n/a	chr6:73330107-73330123
15	RAD21	chr6:73329811-73330233	IMR90	lung:	n/a	chr6:73330179-73330192
16	CUX1	chr6:73329506-73330303	GM12878	blood:	n/a	chr6:73330230-73330244 chr6:73329532-73329541
17	POLR2A	chr6:73329586-73330350	SK-N-MC	brain:	n/a	n/a
18	YY1	chr6:73329538-73330250	GM12878	blood:	n/a	chr6:73329911-73329920
19	RCOR1	chr6:73329620-73330255	GM12878	blood:	n/a	n/a
20	E2F6	chr6:73329822-73330255	K562	blood:	n/a	chr6:73329902-73329914
21	E2F6	chr6:73329857-73330156	K562	blood:	n/a	chr6:73329902-73329914
22	CTCF	chr6:73330033-73330100	NHEK	skin:	n/a	n/a
23	STAT3	chr6:73329713-73330233	GM12878	blood:	n/a	chr6:73329901-73329913
24	KAT2A	chr6:73329913-73330196	GM12878	blood:	n/a	n/a
25	E2F4	chr6:73329789-73330303	GM12878	blood:	n/a	chr6:73329902-73329914
26	USF1	chr6:73329958-73330302	SK-N-SH_RA	brain:	n/a	chr6:73330107-73330123
27	MXI1	chr6:73329924-73330133	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr6:73329490-73330313	GM12878	blood:	n/a	chr6:73329906-73329916
29	POLR2A	chr6:73329752-73330352	GM12878	blood:	n/a	n/a
30	POLR2A	chr6:73329875-73330206	GM12878	blood:	n/a	n/a
31	POU2F2	chr6:73329574-73330311	GM12878	blood:	n/a	chr6:73330109-73330121
32	TAF1	chr6:73329866-73330358	GM12878	blood:	n/a	n/a
33	USF1	chr6:73329951-73330249	H1-hESC	embryonic stem cell:	n/a	chr6:73330107-73330123
34	BCLAF1	chr6:73329558-73330249	GM12878	blood:	n/a	n/a
35	CTCF	chr6:73330060-73330210	HBMEC	blood vessel:	n/a	chr6:73330180-73330193
36	MYC	chr6:73329525-73333814	NB4	blood:	n/a	chr6:73332416-73332426 chr6:73332439-73332454 chr6:73332995-73333005 chr6:73329906-73329916 chr6:73332443-73332450
37	WRNIP1	chr6:73329577-73330551	GM12878	blood:	n/a	n/a
38	TBL1XR1	chr6:73329604-73330398	GM12878	blood:	n/a	n/a
39	SIN3A	chr6:73329941-73330092	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr6:73329751-73330126	GM12878	blood:	n/a	n/a
41	POLR2A	chr6:73329777-73330737	GM12878	blood:	n/a	n/a
42	SMC3	chr6:73329684-73330326	GM12878	blood:	n/a	chr6:73330186-73330194
43	STAT1	chr6:73329774-73330297	GM12878	blood:	n/a	chr6:73329901-73329913
44	POLR2A	chr6:73329848-73330253	GM12878	blood:	n/a	n/a
45	IKZF1	chr6:73329550-73330360	GM12878	blood:	n/a	n/a
46	MYC	chr6:73329762-73330452	K562	blood:	n/a	chr6:73329906-73329916
47	YY1	chr6:73329882-73330305	GM12878	blood:	n/a	chr6:73329911-73329920
48	BACH1	chr6:73330022-73330189	H1-hESC	embryonic stem cell:	n/a	n/a
49	EGR1	chr6:73329818-73330183	GM12878	blood:	n/a	chr6:73330028-73330041 chr6:73329907-73329917 chr6:73330028-73330041 chr6:73330029-73330040 chr6:73330030-73330039 chr6:73329905-73329920 chr6:73330029-73330040 chr6:73330024-73330046 chr6:73330031-73330040 chr6:73330027-73330042 chr6:73329906-73329919 chr6:73330028-73330042 chr6:73330030-73330040 chr6:73330028-73330041 chr6:73330030-73330040
50	PAX5	chr6:73329754-73330092	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:73328381..73330856-chr6:73331571..73334005,2	MCF-7	breast:
2	chr6:73306231..73308470-chr6:73328760..73331273,2	K562	blood:
3	chr6:73121575..73122165-chr6:73329258..73330216,2	K562	blood:
4	chr6:73326755..73329181-chr6:73329336..73331379,2	K562	blood:
5	chr6:73114115..73116045-chr6:73329072..73331095,2	K562	blood:

Variant related genes	Relation type
KCNQ5	TF binding region
ENSG00000185760	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10943047	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11967126	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12110561	1.00[CEU][hapmap]
rs16882670	0.87[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16882707	1.00[CEU][hapmap]
rs2039107	1.00[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28402218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4311478	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4403240	1.00[CEU][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59021804	1.00[EUR][1000 genomes]
rs60563419	1.00[EUR][1000 genomes]
rs60690955	1.00[EUR][1000 genomes]
rs6453595	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6903897	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6918190	1.00[CEU][hapmap]
rs6924417	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73756006	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7749673	1.00[CEU][hapmap]
rs7772464	1.00[EUR][1000 genomes]
rs867520	1.00[CEU][hapmap]
rs9293893	1.00[CEU][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1023809	chr6:73157813-73477997	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv538303	chr6:73157813-73477997	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3347486	chr6:73283590-73445976	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73329200-73330400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
2	chr6:73329200-73331600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr6:73329200-73331600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr6:73329200-73333800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:73329400-73330400	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr6:73329400-73331400	Flanking Active TSS	Primary T cells from cord blood	blood
7	chr6:73329400-73331400	Flanking Active TSS	GM12878-XiMat	blood
8	chr6:73329400-73333200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
9	chr6:73329400-73334400	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr6:73329600-73330200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:73329600-73330200	Flanking Active TSS	HSMMtube	muscle
12	chr6:73329600-73330400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr6:73329600-73330400	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:73329600-73330400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
15	chr6:73329600-73330400	Flanking Active TSS	Fetal Brain Female	brain
16	chr6:73329600-73330400	Flanking Active TSS	Fetal Thymus	thymus
17	chr6:73329600-73330600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
18	chr6:73329600-73330600	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr6:73329600-73330800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:73329600-73330800	Active TSS	Rectal Smooth Muscle	rectum
21	chr6:73329600-73330800	Flanking Active TSS	K562	blood
22	chr6:73329600-73330800	Flanking Active TSS	NHLF	lung
23	chr6:73329600-73331000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
24	chr6:73329600-73331000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr6:73329600-73331000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:73329600-73331000	Enhancers	Liver	Liver
27	chr6:73329600-73331000	Flanking Active TSS	Thymus	Thymus
28	chr6:73329600-73331200	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr6:73329600-73331200	Bivalent Enhancer	Placenta	Placenta
30	chr6:73329600-73331400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr6:73329600-73331600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
32	chr6:73329600-73331600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
33	chr6:73329600-73331600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:73329600-73331600	Flanking Active TSS	HSMM	muscle
35	chr6:73329600-73331800	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr6:73329600-73331800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr6:73329600-73331800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr6:73329600-73331800	Flanking Active TSS	Dnd41	blood
39	chr6:73329600-73331800	Flanking Active TSS	NH-A	brain
40	chr6:73329600-73332000	Active TSS	Brain Hippocampus Middle	brain
41	chr6:73329600-73332400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr6:73329600-73332600	Active TSS	Brain Anterior Caudate	brain
43	chr6:73329600-73332600	Active TSS	Brain Cingulate Gyrus	brain
44	chr6:73329600-73332800	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr6:73329600-73333200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
46	chr6:73329600-73333200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr6:73329600-73333200	Active TSS	Aorta	Aorta
48	chr6:73329600-73333600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
49	chr6:73329600-73333600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:73329600-73333800	Active TSS	Brain Angular Gyrus	brain

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