Variant report

Variant	rs9295338
Chromosome Location	chr6:166796832-166796833
allele	C/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	NFIC	chr6:166796154-166797783	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:166796195-166796927	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr6:166796250-166796849	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr6:166795215-166797378	K562	blood:	n/a	n/a
5	POLR2A	chr6:166796180-166796902	U87	brain:	n/a	n/a
6	E2F4	chr6:166796207-166797476	MCF10A-Er-Src	breast:	n/a	chr6:166796616-166796625 chr6:166796593-166796605 chr6:166796827-166796836 chr6:166796592-166796603
7	POLR2A	chr6:166796526-166796848	A549	lung:	n/a	n/a
8	SIN3AK20	chr6:166795848-166797290	K562	blood:	n/a	n/a
9	STAT5A	chr6:166796030-166797477	GM12878	blood:	n/a	chr6:166796949-166796969
10	CHD2	chr6:166796277-166797120	HepG2	liver:	n/a	n/a
11	ZBTB7A	chr6:166795347-166797515	ECC-1	luminal epithelium:	n/a	chr6:166796136-166796144
12	NFIC	chr6:166796231-166796898	HepG2	liver:	n/a	n/a
13	MAZ	chr6:166795132-166797512	K562	blood:	n/a	chr6:166796913-166796922 chr6:166796910-166796920 chr6:166796909-166796924 chr6:166796911-166796921 chr6:166796907-166796922
14	TAF1	chr6:166796227-166797316	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr6:166795170-166797425	K562	blood:	n/a	chr6:166796913-166796922 chr6:166796910-166796920 chr6:166796909-166796924 chr6:166796911-166796921 chr6:166796907-166796922
16	ZBTB7A	chr6:166795332-166797300	K562	blood:	n/a	chr6:166796136-166796144
17	POLR2A	chr6:166796125-166797312	H1-neurons	neurons:	n/a	n/a
18	NFYB	chr6:166796195-166796893	K562	blood:	n/a	chr6:166796526-166796541 chr6:166796526-166796540 chr6:166796523-166796538 chr6:166796525-166796537 chr6:166796526-166796541
19	POLR2A	chr6:166796190-166796904	GM12878	blood:	n/a	n/a
20	RELA	chr6:166796184-166797345	GM15510	blood:	n/a	n/a
21	TAF1	chr6:166796210-166797156	GM12878	blood:	n/a	n/a
22	MXI1	chr6:166796230-166797254	K562	blood:	n/a	chr6:166796910-166796919 chr6:166796912-166796921
23	POLR2A	chr6:166796181-166797434	K562	blood:	n/a	n/a
24	YY1	chr6:166796065-166797163	K562	blood:	n/a	chr6:166796619-166796633 chr6:166796620-166796634 chr6:166796616-166796625 chr6:166796877-166796891 chr6:166796988-166797002 chr6:166796827-166796836
25	CHD1	chr6:166796680-166797442	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:166796136-166797917	HepG2	liver:	n/a	n/a
27	POLR2A	chr6:166796222-166796858	SK-N-SH	brain:	n/a	n/a
28	SIN3AK20	chr6:166795056-166797610	HCT-116	colon:	n/a	n/a
29	RAD21	chr6:166796750-166797186	H1-hESC	embryonic stem cell:	n/a	chr6:166797093-166797107
30	USF1	chr6:166796777-166797039	SK-N-SH_RA	brain:	n/a	chr6:166796987-166797003
31	MAX	chr6:166796206-166797351	MCF-7	breast:	n/a	chr6:166796913-166796922 chr6:166796910-166796920 chr6:166796909-166796924 chr6:166796911-166796921 chr6:166796907-166796922
32	POLR2A	chr6:166796185-166797460	K562	blood:	n/a	n/a
33	MYC	chr6:166796325-166797412	MCF10A-Er-Src	breast:	n/a	chr6:166796913-166796922 chr6:166796910-166796920 chr6:166796909-166796924 chr6:166796911-166796921 chr6:166796907-166796922
34	CTCF	chr6:166796332-166797551	GM12878	blood:	n/a	chr6:166796776-166796784
35	MYC	chr6:166796377-166796969	HUVEC	blood vessel:	n/a	chr6:166796913-166796922 chr6:166796910-166796920 chr6:166796909-166796924 chr6:166796911-166796921 chr6:166796907-166796922
36	POLR2A	chr6:166795157-166798107	HepG2	liver:	n/a	n/a
37	JUND	chr6:166796735-166797046	H1-hESC	embryonic stem cell:	n/a	n/a
38	CHD2	chr6:166796313-166797263	K562	blood:	n/a	n/a
39	POLR2A	chr6:166796232-166797542	K562	blood:	n/a	n/a
40	POLR2A	chr6:166796145-166796977	ECC-1	luminal epithelium:	n/a	n/a
41	BHLHE40	chr6:166796185-166797343	HepG2	liver:	n/a	chr6:166796445-166796461 chr6:166796987-166797003 chr6:166796619-166796635
42	NR2F2	chr6:166796293-166797186	MCF-7	breast:	n/a	n/a
43	POLR2A	chr6:166796155-166797295	ProgFib	skin:	n/a	n/a
44	SIN3A	chr6:166795266-166797408	GM12878	blood:	n/a	chr6:166796646-166796659 chr6:166796181-166796194 chr6:166796912-166796921
45	USF1	chr6:166796706-166797068	SK-N-SH_RA	brain:	n/a	chr6:166796987-166797003
46	EGR1	chr6:166796783-166797075	GM12878	blood:	n/a	chr6:166796913-166796923 chr6:166796913-166796923 chr6:166796912-166796926 chr6:166796914-166796923
47	POLR2A	chr6:166795156-166797691	HepG2	liver:	n/a	n/a
48	POLR2A	chr6:166796582-166797121	Hela-S3	cervix:	n/a	n/a
49	E2F4	chr6:166796248-166797162	K562	blood:	n/a	chr6:166796616-166796625 chr6:166796593-166796605 chr6:166796827-166796836 chr6:166796592-166796603
50	PML	chr6:166796130-166797414	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:166753320..166757958-chr6:166794622..166799153,8	K562	blood:
2	chr6:166743072..166748840-chr6:166793771..166798653,8	K562	blood:
3	chr6:166754173..166757774-chr6:166795355..166798060,3	MCF-7	breast:
4	chr6:166751804..166757558-chr6:166793969..166799153,5	K562	blood:
5	chr6:166740985..166743870-chr6:166796738..166798607,2	MCF-7	breast:
6	chr6:166796680..166799689-chr6:166808021..166810118,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FGFR1OP-2	chr6:166796677-166798312	ENSG00000261420.1

Variant related genes	Relation type
MPC1	TF binding region
ENSG00000233231	Chromatin interaction
ENSG00000198818	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1546853	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1546854	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1546855	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1569459	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1569460	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1569461	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1977049	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1977050	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1977051	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1977052	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1977053	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1977054	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1977056	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2179177	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2343591	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3734605	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3757194	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3757195	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4305699	0.93[EUR][1000 genomes]
rs4710043	0.95[EUR][1000 genomes]
rs6456078	0.92[EUR][1000 genomes]
rs6456079	0.93[EUR][1000 genomes]
rs6456081	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6905635	0.93[EUR][1000 genomes]
rs6906844	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6912695	0.93[EUR][1000 genomes]
rs6918091	0.81[EUR][1000 genomes]
rs6918135	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7449629	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7744743	0.90[EUR][1000 genomes]
rs7752716	0.87[EUR][1000 genomes]
rs9283865	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9295341	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9295342	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9295343	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9295344	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9295345	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9348123	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9348124	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9348125	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9348126	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9355574	0.90[EUR][1000 genomes]
rs9355575	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9356482	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9356483	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9364845	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9364846	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9364847	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9364848	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9366009	0.93[EUR][1000 genomes]
rs9366010	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	esv3376653	chr6:166783590-166798116	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv3422353	chr6:166794787-166797335	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3329582	chr6:166795187-166797735	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv3340680	chr6:166795587-166798135	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv523548	chr6:166796433-166819774	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166794400-166797600	Active TSS	GM12878-XiMat	blood
2	chr6:166794400-166797800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:166794400-166798000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:166794600-166797600	Active TSS	Psoas Muscle	Psoas
5	chr6:166794600-166797600	Active TSS	Right Ventricle	heart
6	chr6:166794600-166797800	Active TSS	Brain Angular Gyrus	brain
7	chr6:166794600-166797800	Active TSS	NHEK	skin
8	chr6:166794800-166797200	Active TSS	Fetal Stomach	stomach
9	chr6:166794800-166797400	Active TSS	Fetal Muscle Leg	muscle
10	chr6:166794800-166797600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr6:166794800-166797600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:166794800-166797600	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr6:166794800-166797600	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr6:166794800-166797600	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr6:166794800-166797600	Active TSS	Fetal Intestine Large	intestine
16	chr6:166794800-166797600	Active TSS	HSMMtube	muscle
17	chr6:166794800-166797600	Active TSS	K562	blood
18	chr6:166794800-166797600	Active TSS	NHLF	lung
19	chr6:166794800-166797800	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr6:166794800-166797800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:166794800-166797800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr6:166794800-166797800	Active TSS	Stomach Mucosa	stomach
23	chr6:166794800-166798000	Active TSS	Duodenum Mucosa	Duodenum
24	chr6:166795000-166797200	Active TSS	Primary B cells from peripheral blood	blood
25	chr6:166795000-166797200	Active TSS	Fetal Lung	lung
26	chr6:166795000-166797200	Active TSS	Dnd41	blood
27	chr6:166795000-166797400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr6:166795000-166797400	Active TSS	Fetal Muscle Trunk	muscle
29	chr6:166795000-166797400	Active TSS	Placenta Amnion	Placenta Amnion
30	chr6:166795000-166797600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:166795000-166797600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:166795000-166797600	Active TSS	Aorta	Aorta
33	chr6:166795000-166797600	Active TSS	Ovary	ovary
34	chr6:166795000-166797600	Active TSS	A549	lung
35	chr6:166795000-166797600	Active TSS	NHDF-Ad	bronchial
36	chr6:166795000-166797800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:166795000-166797800	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr6:166795000-166797800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:166795000-166797800	Active TSS	Fetal Intestine Small	intestine
40	chr6:166795000-166797800	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr6:166795000-166798000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:166795000-166798000	Active TSS	Brain Hippocampus Middle	brain
43	chr6:166795000-166798000	Active TSS	Colonic Mucosa	Colon
44	chr6:166795000-166798000	Active TSS	Hela-S3	cervix
45	chr6:166795200-166797200	Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr6:166795200-166797400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr6:166795200-166797400	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr6:166795200-166797400	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr6:166795200-166797400	Active TSS	Colon Smooth Muscle	Colon
50	chr6:166795200-166797600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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