Variant report

Variant	rs749621
Chromosome Location	chr6:109762600-109762601
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	ELF1	chr6:109761520-109762968	GM12878	blood:	n/a	chr6:109761858-109761867 chr6:109761854-109761866 chr6:109761795-109761807 chr6:109762102-109762113
2	WRNIP1	chr6:109762542-109762975	GM12878	blood:	n/a	n/a
3	CTCF	chr6:109762500-109762650	WERI-Rb-1	eye:	n/a	n/a
4	KAP1	chr6:109761638-109763030	HEK293	kidney:	n/a	chr6:109761642-109761650
5	CEBPB	chr6:109762405-109762744	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr6:109761401-109763076	H1-neurons	neurons:	n/a	n/a
7	JUND	chr6:109762393-109762635	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr6:109762520-109762670	GM12873	blood:	n/a	n/a
9	RAD21	chr6:109762422-109762752	H1-hESC	embryonic stem cell:	n/a	n/a
10	ELF1	chr6:109762428-109762972	K562	blood:	n/a	n/a
11	E2F6	chr6:109761274-109762704	K562	blood:	n/a	chr6:109761583-109761593 chr6:109761855-109761864 chr6:109761875-109761884 chr6:109761453-109761462 chr6:109761577-109761586 chr6:109761563-109761572 chr6:109762207-109762216 chr6:109762209-109762219
12	CTCF	chr6:109762509-109762690	LNCaP	prostate:	n/a	n/a
13	E2F6	chr6:109761330-109762952	H1-hESC	embryonic stem cell:	n/a	chr6:109761583-109761593 chr6:109761855-109761864 chr6:109761875-109761884 chr6:109761453-109761462 chr6:109761577-109761586 chr6:109761563-109761572 chr6:109762207-109762216 chr6:109762209-109762219
14	POLR2A	chr6:109761490-109762901	MCF-7	breast:	n/a	n/a
15	CTCF	chr6:109762498-109762731	MCF-7	breast:	n/a	n/a
16	POLR2A	chr6:109761435-109763358	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr6:109761614-109762904	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:109761591-109762972	K562	blood:	n/a	n/a
19	MXI1	chr6:109760621-109763112	SK-N-SH	brain:	n/a	chr6:109762145-109762160 chr6:109761832-109761847
20	POLR2A	chr6:109761442-109762808	K562	blood:	n/a	n/a
21	ZBTB7A	chr6:109761331-109762684	K562	blood:	n/a	chr6:109761473-109761487
22	E2F6	chr6:109762502-109762729	K562	blood:	n/a	n/a
23	RCOR1	chr6:109761048-109762700	GM12878	blood:	n/a	n/a
24	CTCF	chr6:109762540-109762690	AG04449	skin:	n/a	n/a
25	CTCF	chr6:109762520-109762670	BJ	skin:	n/a	n/a
26	CTCF	chr6:109762500-109762650	HMEC	breast:	n/a	n/a
27	MYC	chr6:109761346-109762787	K562	blood:	n/a	chr6:109761564-109761574 chr6:109762181-109762190
28	POLR2A	chr6:109761545-109762856	NB4	blood:	n/a	n/a
29	BACH1	chr6:109762430-109762621	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr6:109762580-109762730	GM06990	blood:	n/a	n/a
31	POLR2A	chr6:109762576-109762850	GM12891	blood:	n/a	n/a
32	CTCF	chr6:109762540-109762690	SK-N-SH_RA	brain:	n/a	n/a
33	HCFC1	chr6:109761459-109762696	K562	blood:	n/a	n/a
34	CTCF	chr6:109762520-109762670	HCFaa	heart:	n/a	n/a
35	POLR2A	chr6:109761621-109762691	HepG2	liver:	n/a	n/a
36	POLR2A	chr6:109761555-109762628	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr6:109762480-109762630	SAEC	small airway:	n/a	n/a
38	CTCF	chr6:109762360-109762630	GM12875	blood:	n/a	n/a
39	NRF1	chr6:109762573-109762758	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:109761570-109763535	GM15510	blood:	n/a	n/a
41	ZNF143	chr6:109761497-109762798	GM12878	blood:	n/a	chr6:109761846-109761864
42	CTCF	chr6:109762580-109762730	HL-60	blood:	n/a	n/a
43	TBP	chr6:109760869-109762954	K562	blood:	n/a	n/a
44	CTCF	chr6:109762500-109762650	HUVEC	blood vessel:	n/a	n/a
45	CTCF	chr6:109762491-109762697	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr6:109762520-109762670	RPTEC	kidney:	n/a	n/a
47	CTCF	chr6:109762505-109762682	T-47D	breast:	n/a	n/a
48	CTCF	chr6:109762540-109762652	Pancreas_OC	pancreas:	n/a	n/a
49	CTCF	chr6:109762473-109762718	GM19240	blood:	n/a	n/a
50	SIN3A	chr6:109761593-109762830	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:109759652..109764361-chr6:109800705..109806354,8	K562	blood:
2	chr6:109414651..109418067-chr6:109760738..109763991,4	MCF-7	breast:
3	chr6:109702022..109707287-chr6:109760251..109763953,8	MCF-7	breast:
4	chr6:109759628..109764398-chr6:109803414..109806709,4	K562	blood:
5	chr6:108880181..108882285-chr6:109761167..109763162,2	MCF-7	breast:
6	chr6:109702065..109705528-chr6:109760483..109765471,8	MCF-7	breast:
7	chr6:109760146..109763576-chr6:109804047..109805770,3	MCF-7	breast:
8	chr6:109752212..109757242-chr6:109759553..109764133,7	MCF-7	breast:

Variant related genes	Relation type
PPIL6	TF binding region
SMPD2	TF binding region
ENSG00000112365	Chromatin interaction
ENSG00000185250	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000080546	Chromatin interaction
ENSG00000118689	Chromatin interaction
ENSG00000183137	Chromatin interaction
ENSG00000239160	Chromatin interaction
ENSG00000260273	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10080925	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13437492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1476386	0.87[CEU][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs17070554	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17070590	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1998410	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1998411	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1998813	0.86[CEU][hapmap]
rs2146411	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2177092	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2275649	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3757229	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3757237	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41288560	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4946968	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4946971	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4946972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4946975	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4946977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6907769	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs752260	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9480934	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9480954	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9480959	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs9487074	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9487083	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9487087	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9487099	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9487106	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9487109	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3344959	chr6:109760484-109763032	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:188 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109760200-109763200	Active TSS	A549	lung
2	chr6:109760400-109762600	Active TSS	Ovary	ovary
3	chr6:109760400-109762600	Active TSS	Rectal Smooth Muscle	rectum
4	chr6:109760400-109762800	Active TSS	Fetal Intestine Small	intestine
5	chr6:109760400-109763400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:109760600-109762600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:109760600-109762600	Active TSS	Aorta	Aorta
8	chr6:109760600-109762600	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:109760600-109762600	Active TSS	Fetal Intestine Large	intestine
10	chr6:109760600-109762800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr6:109760800-109762600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:109760800-109762600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:109760800-109762600	Active TSS	Brain Angular Gyrus	brain
14	chr6:109760800-109762600	Active TSS	Brain Cingulate Gyrus	brain
15	chr6:109760800-109762600	Active TSS	Brain Hippocampus Middle	brain
16	chr6:109760800-109762600	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr6:109760800-109762600	Active TSS	Esophagus	oesophagus
18	chr6:109760800-109762600	Active TSS	Pancreas	Pancrea
19	chr6:109760800-109762600	Active TSS	Right Atrium	heart
20	chr6:109760800-109762600	Active TSS	Stomach Mucosa	stomach
21	chr6:109760800-109762600	Active TSS	NHLF	lung
22	chr6:109760800-109762800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr6:109760800-109762800	Active TSS	H9 Cell Line	embryonic stem cell
24	chr6:109760800-109762800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:109760800-109762800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:109760800-109762800	Active TSS	Colon Smooth Muscle	Colon
27	chr6:109760800-109762800	Active TSS	Gastric	stomach
28	chr6:109761000-109762600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:109761000-109762600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:109761000-109762600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:109761000-109762600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:109761000-109762600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:109761000-109762600	Active TSS	Brain Substantia Nigra	brain
34	chr6:109761000-109762600	Active TSS	Left Ventricle	heart
35	chr6:109761000-109762600	Active TSS	Lung	lung
36	chr6:109761000-109762600	Active TSS	Psoas Muscle	Psoas
37	chr6:109761000-109762600	Active TSS	Right Ventricle	heart
38	chr6:109761000-109763000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:109761200-109762600	Active TSS	H1 Cell Line	embryonic stem cell
40	chr6:109761200-109762600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:109761200-109762600	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr6:109761200-109762600	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr6:109761200-109762600	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr6:109761200-109762600	Active TSS	Brain Anterior Caudate	brain
45	chr6:109761200-109762600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:109761200-109762600	Active TSS	Fetal Kidney	kidney
47	chr6:109761200-109762600	Active TSS	Hela-S3	cervix
48	chr6:109761200-109762600	Active TSS	NHDF-Ad	bronchial
49	chr6:109761200-109763000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr6:109761200-109763200	Active TSS	HUES48 Cell Line	embryonic stem cell

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