Variant report

Variant	rs6952476
Chromosome Location	chr7:27778980-27778981
allele	C/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	POLR2A	chr7:27778891-27780253	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr7:27778676-27780760	PBDE	blood:	n/a	n/a
3	POLR2A	chr7:27778869-27780958	MCF10A-Er-Src	breast:	n/a	n/a
4	FOXA2	chr7:27778132-27779219	HepG2	liver:	n/a	n/a
5	SMC3	chr7:27778874-27780695	Hela-S3	cervix:	n/a	n/a
6	CUX1	chr7:27778722-27779015	GM12878	blood:	n/a	n/a
7	POLR2A	chr7:27778927-27780723	K562	blood:	n/a	n/a
8	HCFC1	chr7:27778965-27780872	K562	blood:	n/a	n/a
9	POLR2A	chr7:27778912-27780792	K562	blood:	n/a	n/a
10	KAP1	chr7:27778905-27780728	HEK293	kidney:	n/a	chr7:27780370-27780378
11	MYC	chr7:27778646-27780714	K562	blood:	n/a	chr7:27780133-27780142 chr7:27780137-27780144
12	POLR2A	chr7:27778934-27780798	K562	blood:	n/a	n/a
13	FOXA1	chr7:27778314-27779080	HepG2	liver:	n/a	chr7:27778585-27778600
14	GABPA	chr7:27778753-27780820	SK-N-SH	brain:	n/a	chr7:27780450-27780459
15	MAX	chr7:27778978-27781079	NB4	blood:	n/a	chr7:27780133-27780142 chr7:27780137-27780144
16	CUX1	chr7:27778548-27781013	K562	blood:	n/a	n/a
17	POLR2A	chr7:27778622-27781031	K562	blood:	n/a	n/a
18	NR2F2	chr7:27778937-27780106	K562	blood:	n/a	n/a
19	TBL1XR1	chr7:27778830-27779957	K562	blood:	n/a	n/a
20	MAFK	chr7:27778854-27779848	Hela-S3	cervix:	n/a	n/a
21	TBP	chr7:27778889-27781028	K562	blood:	n/a	n/a
22	POLR2A	chr7:27778856-27780654	HUVEC	blood vessel:	n/a	n/a
23	IRF1	chr7:27778966-27780004	K562	blood:	n/a	chr7:27779143-27779160
24	TCF7L2	chr7:27778870-27781284	Hela-S3	cervix:	n/a	chr7:27781072-27781088 chr7:27778872-27778886 chr7:27781075-27781084
25	MXI1	chr7:27778634-27780856	IMR90	lung:	n/a	n/a
26	BHLHE40	chr7:27778913-27780065	K562	blood:	n/a	n/a
27	RFX5	chr7:27778877-27780836	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr7:27778909-27780307	K562	blood:	n/a	n/a
29	TEAD4	chr7:27778972-27780069	K562	blood:	n/a	n/a
30	GTF2F1	chr7:27778890-27780004	Hela-S3	cervix:	n/a	n/a
31	FOXA1	chr7:27778265-27778983	HepG2	liver:	n/a	chr7:27778585-27778600
32	GATA3	chr7:27778969-27779219	SH-SY5Y	brain:	n/a	n/a
33	POLR2A	chr7:27778885-27780907	K562	blood:	n/a	n/a
34	MAZ	chr7:27778960-27780683	K562	blood:	n/a	chr7:27780133-27780142 chr7:27780137-27780144
35	EP300	chr7:27778460-27779923	K562	blood:	n/a	chr7:27778590-27778600
36	TCF7L2	chr7:27778910-27779598	PANC-1	pancreas:	n/a	n/a
37	REST	chr7:27778928-27780848	H1-neurons	neurons:	n/a	chr7:27779445-27779465 chr7:27780454-27780472
38	GABPA	chr7:27778905-27780817	A549	lung:	n/a	chr7:27780450-27780459
39	POLR2A	chr7:27778893-27780912	NB4	blood:	n/a	n/a
40	TBP	chr7:27778800-27779966	Hela-S3	cervix:	n/a	n/a
41	ARID3A	chr7:27778471-27779883	HepG2	liver:	n/a	n/a
42	POLR2A	chr7:27778949-27780794	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr7:27778911-27780712	HepG2	liver:	n/a	n/a
44	MYBL2	chr7:27778683-27779982	HepG2	liver:	n/a	n/a
45	REST	chr7:27778889-27780397	A549	lung:	n/a	chr7:27779445-27779465
46	POLR2A	chr7:27778842-27780748	SK-N-SH	brain:	n/a	n/a
47	HCFC1	chr7:27778348-27781120	Hela-S3	cervix:	n/a	n/a
48	CCNT2	chr7:27778844-27781091	K562	blood:	n/a	n/a
49	MAX	chr7:27778912-27780931	A549	lung:	n/a	chr7:27780133-27780142 chr7:27780137-27780144
50	MTA3	chr7:27778843-27780797	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:123011130..123011798-chr7:27778729..27779635,2	Hela-S3	cervix:
2	chr7:27778585..27781573-chr7:27808183..27810027,3	MCF-7	breast:
3	chr7:27699948..27706867-chr7:27775418..27784557,21	K562	blood:
4	chr7:27700432..27708426-chr7:27777901..27782637,20	K562	blood:

Variant related genes	Relation type
TAX1BP1	TF binding region
ENSG00000184445	Chromatin interaction
ENSG00000106052	Chromatin interaction
ENSG00000106049	Chromatin interaction
ENSG00000111011	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10486560	0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11981473	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11981639	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11982051	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17155661	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17155671	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17155769	0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17155774	0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17155787	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17155813	0.87[AMR][1000 genomes]
rs17155815	0.87[AMR][1000 genomes]
rs17155818	0.88[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4299908	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4722731	0.88[AFR][1000 genomes]
rs57293935	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57355732	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs59134341	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60524058	1.00[AMR][1000 genomes]
rs60811898	1.00[AMR][1000 genomes]
rs61226834	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6462046	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6942560	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6958438	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6958646	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6963125	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6969000	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs73293835	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73293838	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73293842	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73293856	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73293862	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73293868	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73293882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73293888	0.97[AFR][1000 genomes]
rs73293893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73295504	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73295519	0.89[AMR][1000 genomes]
rs73295543	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73295545	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73295567	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73297523	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73297535	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7783141	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7783426	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7803672	1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1028469	chr7:27767795-27939667	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27774600-27779000	Weak transcription	Small Intestine	intestine
2	chr7:27775800-27779200	Weak transcription	Gastric	stomach
3	chr7:27775800-27779200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:27777400-27779200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:27777800-27781200	Active TSS	K562	blood
6	chr7:27778000-27779000	Weak transcription	Placenta	Placenta
7	chr7:27778200-27779000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr7:27778200-27779000	Active TSS	HepG2	liver
9	chr7:27778200-27780600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:27778400-27779000	Weak transcription	Ovary	ovary
11	chr7:27778400-27779000	Weak transcription	Pancreas	Pancrea
12	chr7:27778400-27779000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr7:27778400-27779600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr7:27778400-27780800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:27778400-27781200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:27778600-27779000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:27778600-27779000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr7:27778600-27779000	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr7:27778600-27779000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:27778600-27779000	Enhancers	Placenta Amnion	Placenta Amnion
21	chr7:27778600-27779000	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr7:27778600-27779000	Flanking Active TSS	A549	lung
23	chr7:27778600-27779000	Flanking Active TSS	Hela-S3	cervix
24	chr7:27778600-27779000	Flanking Active TSS	HMEC	breast
25	chr7:27778600-27779200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr7:27778600-27779200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:27778600-27779200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr7:27778600-27779200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr7:27778600-27779200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:27778600-27779200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr7:27778600-27779200	Flanking Active TSS	Fetal Heart	heart
32	chr7:27778600-27779200	Flanking Active TSS	Fetal Kidney	kidney
33	chr7:27778600-27779200	Flanking Active TSS	NHEK	skin
34	chr7:27778600-27779400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr7:27778600-27779400	Flanking Active TSS	Liver	Liver
36	chr7:27778600-27779400	Active TSS	Brain Germinal Matrix	brain
37	chr7:27778600-27779400	Flanking Active TSS	Dnd41	blood
38	chr7:27778600-27779400	Flanking Active TSS	HUVEC	blood vessel
39	chr7:27778600-27779400	Flanking Active TSS	Osteobl	bone
40	chr7:27778600-27779600	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr7:27778600-27779600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr7:27778600-27779600	Active TSS	Right Atrium	heart
43	chr7:27778600-27780600	Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr7:27778600-27780600	Active TSS	Stomach Smooth Muscle	stomach
45	chr7:27778600-27780800	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr7:27778600-27781000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr7:27778600-27781200	Active TSS	Fetal Intestine Large	intestine
48	chr7:27778600-27781200	Active TSS	Pancreatic Islets	Pancreatic Islet
49	chr7:27778600-27781200	Active TSS	GM12878-XiMat	blood
50	chr7:27778600-27781200	Active TSS	NHLF	lung

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