Variant report

Variant	rs6967996
Chromosome Location	chr7:65905166-65905167
allele	A/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	HNF4A	chr7:65904637-65905166	HepG2	liver:	n/a	chr7:65905032-65905047 chr7:65905065-65905080
2	CTCF	chr7:65905160-65905310	HPAF	blood vessel:	n/a	n/a
3	TEAD4	chr7:65904723-65905200	K562	blood:	n/a	n/a
4	CTCF	chr7:65905140-65905290	HVMF	connective:	n/a	n/a
5	SP1	chr7:65904669-65905176	A549	lung:	n/a	n/a
6	HEY1	chr7:65904487-65905202	HepG2	liver:	n/a	n/a
7	CEBPB	chr7:65904797-65905170	HepG2	liver:	n/a	n/a
8	FOXA2	chr7:65904633-65905249	A549	lung:	n/a	n/a
9	ARID3A	chr7:65904544-65905227	HepG2	liver:	n/a	n/a
10	NFIC	chr7:65903429-65905219	HepG2	liver:	n/a	n/a
11	FOXA2	chr7:65903559-65905183	HepG2	liver:	n/a	n/a
12	GATA1	chr7:65904646-65905395	K562	blood:	n/a	chr7:65904977-65904986 chr7:65904797-65904806 chr7:65904974-65904990 chr7:65904979-65904986 chr7:65904977-65904987
13	FOSL2	chr7:65904493-65905177	HepG2	liver:	n/a	chr7:65904795-65904804 chr7:65904793-65904804 chr7:65905091-65905100 chr7:65904797-65904804
14	CTCF	chr7:65905160-65905310	HepG2	liver:	n/a	n/a
15	TEAD4	chr7:65904451-65905444	HepG2	liver:	n/a	n/a
16	HNF4A	chr7:65904746-65905332	HepG2	liver:	n/a	chr7:65905032-65905047 chr7:65905065-65905080
17	FOXA1	chr7:65904541-65905188	HepG2	liver:	n/a	n/a
18	RCOR1	chr7:65904552-65905181	IMR90	lung:	n/a	n/a
19	MYBL2	chr7:65903332-65905445	HepG2	liver:	n/a	n/a
20	CBX3	chr7:65904776-65905196	K562	blood:	n/a	n/a
21	CTCF	chr7:65905160-65905310	BJ	skin:	n/a	n/a
22	FOXA1	chr7:65904461-65905288	HepG2	liver:	n/a	n/a
23	EP300	chr7:65904794-65905166	K562	blood:	n/a	chr7:65904795-65904804
24	EP300	chr7:65904548-65905220	HepG2	liver:	n/a	chr7:65904795-65904804
25	FOXA1	chr7:65904591-65905220	HepG2	liver:	n/a	n/a
26	SP1	chr7:65904494-65905257	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000236928	TF binding region

Extended variants
information (count: 83 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10755833	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10950041	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12532998	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12533997	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12535036	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12668936	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12673810	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12698520	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12698521	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12698523	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13309022	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1363055	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1807064	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1833495	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1968225	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1974769	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1981798	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1981799	0.82[AMR][1000 genomes]
rs2042133	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2077593	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2161065	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2277911	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2420591	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2420599	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34406470	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35149210	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35410151	0.84[AFR][1000 genomes]
rs3735148	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3857684	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3981131	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4717292	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4717299	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4717300	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4718343	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4718344	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4718349	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4718357	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4718358	0.85[EUR][1000 genomes]
rs60193905	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6460295	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6460296	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6460300	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6945019	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6945032	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6949920	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6957199	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6958271	0.80[AFR][1000 genomes]
rs6961155	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6961990	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6970030	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6970357	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6970860	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6978429	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6979382	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7781061	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7781698	0.81[AMR][1000 genomes]
rs778692	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs778694	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs778695	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs778699	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs778700	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs778706	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs778708	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs778710	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs778712	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs778721	0.81[AMR][1000 genomes]
rs7788984	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7789554	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7789768	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7799834	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7803416	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7803424	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9691480	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9791895	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv1802195	chr7:65886451-65945211	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1027068	chr7:65901543-65991211	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv966832	chr7:65901934-65916028	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs6967996	RP4-756H11.3	cis	lung	GTEx
rs6967996	RP4-756H11.3	cis	Thyroid	GTEx
rs6967996	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs6967996	RNU6-96P	cis	Thyroid	GTEx
rs6967996	GS1-124K5.4	cis	Whole Blood	GTEx
rs6967996	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs6967996	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs6967996	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs6967996	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6967996	GTF2IRD1P1	cis	Thyroid	GTEx
rs6967996	RP4-756H11.3	cis	Artery Tibial	GTEx
rs6967996	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs6967996	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs6967996	RP4-756H11.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65879000-65905600	Weak transcription	Lung	lung
2	chr7:65879000-65909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:65879000-65922200	Weak transcription	Small Intestine	intestine
4	chr7:65879200-65907400	Weak transcription	Esophagus	oesophagus
5	chr7:65879200-65924600	Weak transcription	Brain Anterior Caudate	brain
6	chr7:65879200-65939800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr7:65879200-65946000	Weak transcription	NHEK	skin
8	chr7:65879200-65957600	Weak transcription	Psoas Muscle	Psoas
9	chr7:65879400-65909200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr7:65879400-65914200	Weak transcription	Left Ventricle	heart
11	chr7:65879400-65914200	Weak transcription	GM12878-XiMat	blood
12	chr7:65879400-65917200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:65879400-65921000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr7:65879400-65921400	Weak transcription	Fetal Kidney	kidney
15	chr7:65879600-65907600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr7:65879600-65913600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr7:65879600-65919000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr7:65879600-65920400	Weak transcription	Primary B cells from cord blood	blood
19	chr7:65879800-65913600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr7:65884000-65919600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr7:65886000-65913600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr7:65886600-65920400	Weak transcription	Right Ventricle	heart
23	chr7:65887000-65924600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr7:65887000-65924600	Weak transcription	Brain Hippocampus Middle	brain
25	chr7:65889200-65939600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr7:65889600-65913800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr7:65890000-65928800	Weak transcription	Adipose Nuclei	Adipose
28	chr7:65890200-65907400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr7:65890400-65916200	Weak transcription	Fetal Thymus	thymus
30	chr7:65891600-65939000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr7:65892000-65931800	Weak transcription	Ovary	ovary
32	chr7:65893200-65913400	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr7:65894200-65905400	Weak transcription	Gastric	stomach
34	chr7:65894200-65939200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr7:65894600-65905200	Weak transcription	Pancreas	Pancrea
36	chr7:65894800-65914000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr7:65895200-65913400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr7:65895400-65907400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr7:65895800-65905200	Weak transcription	Fetal Intestine Large	intestine
40	chr7:65897600-65913200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:65898200-65938200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:65900000-65907600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr7:65900200-65913600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:65900200-65913800	Weak transcription	Fetal Stomach	stomach
45	chr7:65900400-65911000	Weak transcription	Fetal Muscle Leg	muscle
46	chr7:65900800-65912200	Weak transcription	Primary T cells from cord blood	blood
47	chr7:65902400-65905600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr7:65902600-65905800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr7:65902600-65906000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr7:65903000-65922000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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