Variant report

Variant	rs71535635
Chromosome Location	chr7:66313891-66313892
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	E2F4	chr7:66313540-66313921	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr7:66313307-66313908	HUVEC	blood vessel:	n/a	chr7:66313655-66313662 chr7:66313652-66313664 chr7:66313653-66313662 chr7:66313732-66313744 chr7:66313652-66313663 chr7:66313651-66313659
3	FOS	chr7:66313431-66313898	MCF10A-Er-Src	breast:	n/a	chr7:66313655-66313662 chr7:66313652-66313664 chr7:66313653-66313662 chr7:66313732-66313744 chr7:66313652-66313663 chr7:66313651-66313659
4	JUND	chr7:66313339-66313894	SK-N-SH	brain:	n/a	chr7:66313655-66313662 chr7:66313652-66313664 chr7:66313653-66313662 chr7:66313732-66313744 chr7:66313652-66313663 chr7:66313651-66313659

No.	Distal block	Cell Line	Cell type
1	chr7:66309053..66311838-chr7:66313170..66315306,3	K562	blood:
2	chr7:66308221..66311838-chr7:66312285..66316374,5	K562	blood:
3	chr7:66312126..66314998-chr7:66385416..66387725,2	MCF-7	breast:

Variant related genes	Relation type
GTF2IRD1P1	TF binding region
ENSG00000230583	Chromatin interaction
ENSG00000106609	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1267817	0.95[AFR][1000 genomes]
rs1267818	0.95[AFR][1000 genomes]
rs12698542	0.95[AFR][1000 genomes]
rs12698551	0.88[ASN][1000 genomes]
rs13228779	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13229468	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13232393	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13233569	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13235282	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13236129	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13237544	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13238478	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13238612	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1573944	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1618893	0.95[AFR][1000 genomes]
rs1638731	0.86[AFR][1000 genomes]
rs1638734	0.95[AFR][1000 genomes]
rs1880644	0.85[AFR][1000 genomes]
rs1882655	0.95[AFR][1000 genomes]
rs1922723	0.95[AFR][1000 genomes]
rs2141924	0.95[AFR][1000 genomes]
rs2178742	0.95[AFR][1000 genomes]
rs2659903	0.95[AFR][1000 genomes]
rs2659911	0.95[AFR][1000 genomes]
rs2659913	0.95[AFR][1000 genomes]
rs2707823	0.95[AFR][1000 genomes]
rs2707826	0.86[AFR][1000 genomes]
rs2707828	0.85[AFR][1000 genomes]
rs2707830	0.95[AFR][1000 genomes]
rs2707832	0.95[AFR][1000 genomes]
rs2707833	0.83[AFR][1000 genomes]
rs2707838	0.95[AFR][1000 genomes]
rs2707840	0.95[AFR][1000 genomes]
rs34162778	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34314366	0.85[AFR][1000 genomes]
rs34423980	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs34559676	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34785430	0.85[AFR][1000 genomes]
rs34816289	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs35043782	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs35111158	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs35315599	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35390465	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35481333	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35508430	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35624856	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35676956	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35821254	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs35851021	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36059333	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3936	0.95[AFR][1000 genomes]
rs4457208	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs55849324	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55889925	0.88[ASN][1000 genomes]
rs56006261	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56235846	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56675463	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59308022	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60201031	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60326618	0.95[AFR][1000 genomes]
rs6460312	0.95[AFR][1000 genomes]
rs66510832	0.81[ASN][1000 genomes]
rs67319329	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs71535634	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71563136	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs869249	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs876743	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv981514	chr7:66310139-66366240	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs71535635	VKORC1L1	cis	Whole Blood	GTEx
rs71535635	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs71535635	GUSB	cis	Whole Blood	GTEx
rs71535635	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs71535635	RP4-756H11.3	cis	lung	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66310400-66337000	Weak transcription	Small Intestine	intestine
2	chr7:66310600-66329200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:66310800-66314600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr7:66310800-66324800	Weak transcription	Brain Substantia Nigra	brain
5	chr7:66310800-66331600	Weak transcription	Ovary	ovary
6	chr7:66311000-66314000	Weak transcription	Fetal Intestine Small	intestine
7	chr7:66311000-66322400	Weak transcription	Placenta	Placenta
8	chr7:66311000-66323400	Weak transcription	Lung	lung
9	chr7:66311000-66323600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:66311000-66323600	Weak transcription	Primary T cells from cord blood	blood
11	chr7:66311000-66324200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr7:66311000-66324400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr7:66311000-66324600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr7:66311000-66324600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr7:66311000-66324600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr7:66311000-66324600	Weak transcription	Left Ventricle	heart
17	chr7:66311000-66324600	Weak transcription	Psoas Muscle	Psoas
18	chr7:66311000-66324800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:66311000-66324800	Weak transcription	Brain Hippocampus Middle	brain
20	chr7:66311000-66324800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr7:66311000-66325200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr7:66311000-66329000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:66311000-66332600	Weak transcription	Colonic Mucosa	Colon
24	chr7:66311000-66339200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr7:66311000-66345800	Weak transcription	HSMMtube	muscle
26	chr7:66311000-66349400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:66311000-66358400	Weak transcription	Brain Anterior Caudate	brain
28	chr7:66311000-66368000	Weak transcription	Colon Smooth Muscle	Colon
29	chr7:66311000-66385200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr7:66311200-66322000	Weak transcription	Liver	Liver
31	chr7:66311200-66322600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr7:66311200-66322800	Weak transcription	Fetal Muscle Leg	muscle
33	chr7:66311200-66323600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr7:66311200-66324000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr7:66311200-66324200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr7:66311200-66324200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr7:66311200-66324600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:66311200-66324600	Weak transcription	Esophagus	oesophagus
39	chr7:66311200-66324600	Weak transcription	Pancreas	Pancrea
40	chr7:66311200-66324800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:66311200-66324800	Weak transcription	Adipose Nuclei	Adipose
42	chr7:66311200-66324800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr7:66311200-66324800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr7:66311200-66324800	Weak transcription	Right Ventricle	heart
45	chr7:66311200-66324800	Weak transcription	Spleen	Spleen
46	chr7:66311200-66343000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr7:66311200-66385200	Weak transcription	Brain Angular Gyrus	brain
48	chr7:66311400-66324800	Weak transcription	Gastric	stomach
49	chr7:66311600-66324600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr7:66311600-66334000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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