Variant report

Variant	rs36104268
Chromosome Location	chr7:65955059-65955060
allele	A/C
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	FOSL2	chr7:65954804-65955104	HepG2	liver:	n/a	chr7:65954834-65954846
2	FOSL2	chr7:65954799-65955149	HepG2	liver:	n/a	chr7:65954834-65954846
3	FOXA1	chr7:65954771-65955225	HepG2	liver:	n/a	n/a
4	FOXA1	chr7:65954823-65955201	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GUSB-14	chr7:65954925-65955094	NONHSAT121187

Variant related genes	Relation type
ENSG00000230189	TF binding region
ENSG00000244657	TF binding region
ENSG00000237310	TF binding region

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10247526	0.90[AFR][1000 genomes]
rs10807702	0.90[AFR][1000 genomes]
rs10950032	0.90[AFR][1000 genomes]
rs1267816	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1267817	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1267818	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1267819	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1267820	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13222887	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13224048	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13232193	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13235972	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13237037	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13237344	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13241548	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13242216	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1392104	0.82[AFR][1000 genomes]
rs1499613	0.82[AFR][1000 genomes]
rs1499614	0.82[AFR][1000 genomes]
rs1553174	0.82[AFR][1000 genomes]
rs1618893	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1638731	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1638734	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1796215	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1796220	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1796228	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1882655	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2533287	0.84[EUR][1000 genomes]
rs2533288	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2659911	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2659913	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2707828	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2707830	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2707831	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2707832	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2707833	0.87[AFR][1000 genomes]
rs2707838	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2707840	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2707844	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs34192067	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34363376	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34700450	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34807232	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35261784	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35370033	0.81[EUR][1000 genomes]
rs35823062	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35825036	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3936	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4718333	0.90[AFR][1000 genomes]
rs58668827	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58669269	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60326618	1.00[AFR][1000 genomes]
rs6460312	1.00[AFR][1000 genomes]
rs66630579	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6958420	0.82[AFR][1000 genomes]
rs6964245	0.91[AFR][1000 genomes]
rs6964530	1.00[AFR][1000 genomes]
rs71563118	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73135918	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs73150635	0.82[ASN][1000 genomes]
rs778679	0.91[AFR][1000 genomes]
rs778683	0.91[AFR][1000 genomes]
rs778687	0.83[AFR][1000 genomes]
rs778691	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs778693	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs778701	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs778704	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs778729	0.82[AFR][1000 genomes]
rs778732	0.90[AFR][1000 genomes]
rs778733	0.82[AFR][1000 genomes]
rs7792391	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
8	esv3447484	chr7:65909457-66033145	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	esv3377926	chr7:65934493-66051484	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv888327	chr7:65938980-66029429	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised 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	29 gene(s)	inside rSNPs	diseases
11	esv3423847	chr7:65941210-66054107	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv981508	chr7:65941357-65958736	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs36104268	VKORC1L1	cis	Whole Blood	GTEx
rs36104268	GUSB	cis	Whole Blood	GTEx
rs36104268	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs36104268	RP4-756H11.3	cis	lung	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65879200-65957600	Weak transcription	Psoas Muscle	Psoas
2	chr7:65905600-65957600	Weak transcription	Fetal Lung	lung
3	chr7:65911400-65957800	Weak transcription	Aorta	Aorta
4	chr7:65917000-65957800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr7:65925000-65957200	Weak transcription	Dnd41	blood
6	chr7:65925000-65957600	Weak transcription	Left Ventricle	heart
7	chr7:65925400-65955400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr7:65925400-65957200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr7:65927600-65957600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr7:65931200-65957600	Weak transcription	Right Ventricle	heart
11	chr7:65931400-65957800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr7:65934600-65955200	Weak transcription	HMEC	breast
13	chr7:65935800-65957600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr7:65937200-65957200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr7:65937200-65957200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr7:65937200-65957600	Weak transcription	HSMMtube	muscle
17	chr7:65937400-65957200	Weak transcription	Right Atrium	heart
18	chr7:65937600-65958000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:65937800-65956600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr7:65937800-65957600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:65937800-65957800	Weak transcription	Fetal Kidney	kidney
22	chr7:65937800-65957800	Weak transcription	Small Intestine	intestine
23	chr7:65938200-65957600	Weak transcription	HSMM	muscle
24	chr7:65938800-65957600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr7:65939200-65957600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr7:65939400-65957600	Weak transcription	Brain Germinal Matrix	brain
27	chr7:65940200-65957200	Weak transcription	Brain Substantia Nigra	brain
28	chr7:65940400-65957600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:65940600-65957400	Weak transcription	Pancreas	Pancrea
30	chr7:65940600-65957600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr7:65940800-65957200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr7:65940800-65957600	Weak transcription	Brain Hippocampus Middle	brain
33	chr7:65940800-65957600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr7:65941000-65957200	Weak transcription	Gastric	stomach
35	chr7:65941000-65957400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr7:65941000-65957600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:65941000-65957600	Weak transcription	Spleen	Spleen
38	chr7:65941400-65957600	Weak transcription	Colon Smooth Muscle	Colon
39	chr7:65941600-65957600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr7:65942200-65955600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr7:65942800-65957600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr7:65943400-65957400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr7:65943400-65957600	Weak transcription	GM12878-XiMat	blood
44	chr7:65943600-65957600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr7:65943800-65957400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr7:65944000-65957600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:65944200-65957400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr7:65944200-65957400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr7:65944200-65957600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr7:65944200-65957600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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