Variant report

Variant	rs883632
Chromosome Location	chr6:73331258-73331259
allele	G/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	CTBP2	chr6:73330636-73333123	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:73331067-73333300	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr6:73330981-73331581	GM12878	blood:	n/a	n/a
4	CTCF	chr6:73331180-73331330	HMEC	breast:	n/a	chr6:73331239-73331252
5	CTCF	chr6:73331220-73331370	HEK293	kidney:	n/a	chr6:73331239-73331252
6	ESR1	chr6:73331163-73331464	T-47D	breast:	n/a	n/a
7	POLR2A	chr6:73329493-73333253	NB4	blood:	n/a	n/a
8	SMC3	chr6:73331074-73331706	GM12878	blood:	n/a	n/a
9	ZNF143	chr6:73331182-73333246	GM12878	blood:	n/a	chr6:73333025-73333035 chr6:73331594-73331612
10	POLR2A	chr6:73330933-73331590	SK-N-SH	brain:	n/a	n/a
11	EBF1	chr6:73331082-73331469	GM12878	blood:	n/a	n/a
12	CHD1	chr6:73331153-73333968	GM12878	blood:	n/a	chr6:73332987-73332997
13	ESR1	chr6:73331162-73331496	T-47D	breast:	n/a	n/a
14	CTCF	chr6:73331160-73331310	HBMEC	blood vessel:	n/a	chr6:73331239-73331252
15	POLR2A	chr6:73330620-73333240	GM18951	blood:	n/a	n/a
16	FOXP2	chr6:73331017-73331600	PFSK-1	brain:	n/a	n/a
17	SETDB1	chr6:73331048-73331350	U2OS	brain:	n/a	n/a
18	E2F6	chr6:73330955-73333250	K562	blood:	n/a	chr6:73331774-73331786 chr6:73331109-73331121 chr6:73331735-73331742 chr6:73331865-73331875 chr6:73332986-73332998 chr6:73332986-73332995 chr6:73331777-73331786 chr6:73331734-73331746 chr6:73331735-73331742 chr6:73331735-73331742
19	ZEB1	chr6:73331050-73331928	GM12878	blood:	n/a	n/a
20	EBF1	chr6:73331209-73331409	GM12878	blood:	n/a	n/a
21	ESR1	chr6:73331187-73331537	T-47D	breast:	n/a	n/a
22	POLR2A	chr6:73330723-73333369	SK-N-MC	brain:	n/a	n/a
23	SIN3AK20	chr6:73331118-73331544	SK-N-SH	brain:	n/a	n/a
24	TCF12	chr6:73330971-73334035	SK-N-SH	brain:	n/a	chr6:73331770-73331780 chr6:73332947-73332957
25	MYC	chr6:73329525-73333814	NB4	blood:	n/a	chr6:73332416-73332426 chr6:73332439-73332454 chr6:73332995-73333005 chr6:73329906-73329916 chr6:73332443-73332450
26	POLR2A	chr6:73331086-73331428	GM12878	blood:	n/a	n/a
27	SUZ12	chr6:73330666-73332359	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr6:73331160-73331310	GM12865	blood:	n/a	chr6:73331239-73331252
29	TAF1	chr6:73331131-73331476	SK-N-SH	brain:	n/a	n/a
30	STAT1	chr6:73330901-73331451	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:73330912-73333393	GM12878	blood:	n/a	n/a
32	EP300	chr6:73330803-73333357	SK-N-SH	brain:	n/a	chr6:73333212-73333222
33	POLR2A	chr6:73331010-73331510	Gliobla	brain:	n/a	n/a
34	SIN3A	chr6:73331127-73333048	H1-hESC	embryonic stem cell:	n/a	chr6:73331862-73331875 chr6:73331877-73331886 chr6:73332980-73332991
35	TCF7L2	chr6:73331142-73331448	PANC-1	pancreas:	n/a	n/a
36	MYC	chr6:73331100-73331360	MCF-7	breast:	n/a	n/a
37	TBL1XR1	chr6:73331147-73332034	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:73331216-73331267	MCF-7	breast:	n/a	n/a
39	POLR2A	chr6:73330634-73333819	Raji	blood:	n/a	n/a
40	E2F6	chr6:73330724-73333226	H1-hESC	embryonic stem cell:	n/a	chr6:73331774-73331786 chr6:73331109-73331121 chr6:73331735-73331742 chr6:73331865-73331875 chr6:73332986-73332998 chr6:73332986-73332995 chr6:73331777-73331786 chr6:73331734-73331746 chr6:73331735-73331742 chr6:73331735-73331742
41	YY1	chr6:73330955-73332712	SK-N-SH	brain:	n/a	chr6:73331874-73331888 chr6:73331868-73331882 chr6:73331864-73331878 chr6:73332473-73332484 chr6:73331777-73331786 chr6:73331861-73331872
42	MAX	chr6:73331043-73331534	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr6:73331029-73331309	MCF-7	breast:	n/a	n/a
44	CTCF	chr6:73331240-73331390	BJ	skin:	n/a	n/a
45	CTCF	chr6:73331235-73331413	NHEK	skin:	n/a	chr6:73331239-73331252
46	MAX	chr6:73331091-73332772	H1-hESC	embryonic stem cell:	n/a	chr6:73332416-73332426 chr6:73332439-73332454 chr6:73332443-73332450
47	POLR2A	chr6:73331045-73331584	ProgFib	skin:	n/a	n/a
48	PML	chr6:73331124-73332121	GM12878	blood:	n/a	chr6:73331631-73331639
49	HMGN3	chr6:73330998-73332550	K562	blood:	n/a	n/a
50	ELF1	chr6:73330586-73333174	GM12878	blood:	n/a	chr6:73331869-73331881

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:73331238-73331288	Caco-2	colon:	n/a
2	chr6:73331238-73331288	K562	blood:	n/a
3	chr6:73331238-73331288	ProgFib	skin:	n/a
4	chr6:73331238-73331288	GM12892	blood:	n/a
5	chr6:73331238-73331288	H1-hESC	embryonic stem cell:	embryo
6	chr6:73331238-73331288	T-47D	breast:	n/a
7	chr6:73331238-73331288	U87	brain:	n/a
8	chr6:73331238-73331288	HPAEpiC	pulmonary alveolar:	n/a
9	chr6:73331238-73331288	HUVEC	blood vessel:	n/a
10	chr6:73331238-73331288	AG10803	skin:	n/a
11	chr6:73331238-73331288	HCF	heart:	n/a
12	chr6:73331238-73331288	NB4	blood:	n/a
13	chr6:73331238-73331288	HNPCEpiC	eye:	n/a
14	chr6:73331238-73331288	HCPEpiC	choroid plexus:	n/a
15	chr6:73331238-73331288	AoSMC	blood vessel:	n/a
16	chr6:73331238-73331288	HCM	heart:	n/a
17	chr6:73331238-73331288	SK-N-MC	brain:	n/a
18	chr6:73331238-73331288	A549	lung:	n/a
19	chr6:73331238-73331288	HEEpiC	esophagus:	n/a
20	chr6:73331238-73331288	BE2_C	brain:	n/a
21	chr6:73331238-73331288	PFSK-1	brain:	n/a
22	chr6:73331238-73331288	NHBE	bronchial:	n/a
23	chr6:73331238-73331288	AG04450	lung:	fetal
24	chr6:73331238-73331288	BJ	skin:	n/a
25	chr6:73331238-73331288	RPTEC	kidney:	n/a
26	chr6:73331238-73331288	HRPEpiC	eye:	n/a
27	chr6:73331238-73331288	SKMC	muscle:	n/a
28	chr6:73331238-73331288	GM06990	blood:	n/a
29	chr6:73331238-73331288	PrEC	prostate:	n/a
30	chr6:73331238-73331288	GM12878	blood:	n/a
31	chr6:73331238-73331288	HEK293	kidney:	embryo
32	chr6:73331238-73331288	Hela-S3	cervix:	n/a
33	chr6:73331238-73331288	NHDF-neo	bronchial:	n/a
34	chr6:73331238-73331288	AG09309	skin:	n/a
35	chr6:73331238-73331288	GM12891	blood:	n/a
36	chr6:73331238-73331288	HRCEpiC	kidney:	n/a
37	chr6:73331238-73331288	Hepatocyte	liver:	n/a
38	chr6:73331238-73331288	GM19239	blood:	n/a
39	chr6:73331238-73331288	Jurkat	blood:	n/a
40	chr6:73331238-73331288	AG09319	gingival:	n/a
41	chr6:73331238-73331288	SAEC	small airway:	n/a
42	chr6:73331238-73331288	NT2-D1	testis:	n/a
43	chr6:73331238-73331288	SK-N-SH	brain:	n/a
44	chr6:73331238-73331288	IMR90	lung:	fetal
45	chr6:73331238-73331288	LNCaP	prostate:	n/a
46	chr6:73331238-73331288	AG04449	skin:	fetal
47	chr6:73331238-73331288	NH-A	brain:	n/a
48	chr6:73331238-73331288	HMEC	breast:	n/a
49	chr6:73331238-73331288	SK-N-SH_RA	brain:	n/a
50	chr6:73331238-73331288	HIPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:73306231..73308470-chr6:73328760..73331273,2	K562	blood:
2	chr6:73326755..73329181-chr6:73329336..73331379,2	K562	blood:
3	chr11:62608699..62609218-chr6:73330653..73331386,2	NB4	blood:

Variant related genes	Relation type
KCNQ5	TF binding region
KCNQ5	CpG island

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10805964	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10943042	0.89[ASN][1000 genomes]
rs10943044	0.89[ASN][1000 genomes]
rs10943046	0.91[ASN][1000 genomes]
rs12111265	0.85[ASN][1000 genomes]
rs12175038	0.89[ASN][1000 genomes]
rs12523691	0.83[ASN][1000 genomes]
rs12528674	0.89[ASN][1000 genomes]
rs13213217	0.88[ASN][1000 genomes]
rs1543621	0.88[ASN][1000 genomes]
rs16882711	0.87[ASN][1000 genomes]
rs17692121	0.89[ASN][1000 genomes]
rs1884090	0.83[ASN][1000 genomes]
rs3734212	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3936157	0.83[ASN][1000 genomes]
rs4707978	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4707980	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4707981	0.83[ASN][1000 genomes]
rs4707983	0.81[ASN][1000 genomes]
rs67188382	0.81[ASN][1000 genomes]
rs67895524	0.94[ASN][1000 genomes]
rs68141942	0.92[ASN][1000 genomes]
rs6899573	0.88[ASN][1000 genomes]
rs6900054	0.88[ASN][1000 genomes]
rs6900100	0.87[ASN][1000 genomes]
rs6900103	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6913237	0.87[ASN][1000 genomes]
rs6915647	0.81[ASN][1000 genomes]
rs6917707	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6922044	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6926943	0.94[ASN][1000 genomes]
rs6931363	0.88[ASN][1000 genomes]
rs6937158	0.89[ASN][1000 genomes]
rs6937341	0.89[ASN][1000 genomes]
rs7451091	0.83[ASN][1000 genomes]
rs769133	0.83[ASN][1000 genomes]
rs7742742	0.80[ASN][1000 genomes]
rs7749079	0.93[ASN][1000 genomes]
rs7749264	0.92[ASN][1000 genomes]
rs7760979	0.91[ASN][1000 genomes]
rs7768117	0.92[ASN][1000 genomes]
rs7771839	0.83[ASN][1000 genomes]
rs7772714	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7776102	0.83[ASN][1000 genomes]
rs867521	0.90[ASN][1000 genomes]
rs883631	0.88[ASN][1000 genomes]
rs9293894	0.82[ASN][1000 genomes]
rs9293898	0.80[ASN][1000 genomes]
rs9293899	0.85[ASN][1000 genomes]
rs9342961	0.87[ASN][1000 genomes]
rs9342962	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9360570	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9360571	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9360572	0.89[ASN][1000 genomes]
rs9360573	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9360580	0.88[ASN][1000 genomes]
rs9360584	0.92[ASN][1000 genomes]
rs9360587	0.89[ASN][1000 genomes]
rs9360588	0.81[ASN][1000 genomes]
rs9442830	0.97[ASN][1000 genomes]
rs9442831	0.97[ASN][1000 genomes]
rs9442832	0.92[ASN][1000 genomes]
rs9442834	0.89[ASN][1000 genomes]
rs9442835	0.89[ASN][1000 genomes]
rs9446734	0.83[ASN][1000 genomes]
rs9446735	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3412497	chr6:73330856-73333404	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73329200-73331600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr6:73329200-73331600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr6:73329200-73333800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:73329400-73331400	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr6:73329400-73331400	Flanking Active TSS	GM12878-XiMat	blood
6	chr6:73329400-73333200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
7	chr6:73329400-73334400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr6:73329600-73331400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
9	chr6:73329600-73331600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
10	chr6:73329600-73331600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
11	chr6:73329600-73331600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:73329600-73331600	Flanking Active TSS	HSMM	muscle
13	chr6:73329600-73331800	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr6:73329600-73331800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr6:73329600-73331800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr6:73329600-73331800	Flanking Active TSS	Dnd41	blood
17	chr6:73329600-73331800	Flanking Active TSS	NH-A	brain
18	chr6:73329600-73332000	Active TSS	Brain Hippocampus Middle	brain
19	chr6:73329600-73332400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:73329600-73332600	Active TSS	Brain Anterior Caudate	brain
21	chr6:73329600-73332600	Active TSS	Brain Cingulate Gyrus	brain
22	chr6:73329600-73332800	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr6:73329600-73333200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:73329600-73333200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr6:73329600-73333200	Active TSS	Aorta	Aorta
26	chr6:73329600-73333600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr6:73329600-73333600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr6:73329600-73333800	Active TSS	Brain Angular Gyrus	brain
29	chr6:73329800-73331400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:73329800-73331400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:73329800-73331800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:73329800-73331800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr6:73329800-73332800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:73329800-73333200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
35	chr6:73329800-73333200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
36	chr6:73329800-73333200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
37	chr6:73329800-73333200	Active TSS	Psoas Muscle	Psoas
38	chr6:73329800-73333400	Active TSS	Primary T killer memory cells from peripheral blood	blood
39	chr6:73329800-73333400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:73330000-73331800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
41	chr6:73330000-73332400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:73330000-73332400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
43	chr6:73330000-73333200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
44	chr6:73330200-73333200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:73330400-73331800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:73330400-73331800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
47	chr6:73330400-73333000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr6:73330600-73331400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
49	chr6:73330600-73331400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:73330600-73331400	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon

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