Variant report

Variant	rs13238612
Chromosome Location	chr7:66333958-66333959
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66333809..66336428-chr7:66342032..66344327,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs12698542	0.86[AFR][1000 genomes]
rs12698551	0.90[ASN][1000 genomes]
rs13228779	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13229468	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13232393	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13233569	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13235282	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13236129	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13237544	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13238478	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13246227	0.88[EUR][1000 genomes]
rs1573944	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1882655	0.86[AFR][1000 genomes]
rs1922723	0.86[AFR][1000 genomes]
rs2141924	0.86[AFR][1000 genomes]
rs2178742	0.86[AFR][1000 genomes]
rs2659903	0.86[AFR][1000 genomes]
rs2659911	0.86[AFR][1000 genomes]
rs2659913	0.86[AFR][1000 genomes]
rs2707823	0.86[AFR][1000 genomes]
rs2707830	0.86[AFR][1000 genomes]
rs2707832	0.86[AFR][1000 genomes]
rs2707838	0.86[AFR][1000 genomes]
rs2707840	0.86[AFR][1000 genomes]
rs34162778	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34314366	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs34423980	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34559676	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34785430	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34816289	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35043782	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35111158	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35315599	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35390465	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35481333	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35508430	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35624856	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35676956	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35821254	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35851021	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs36059333	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3936	0.86[AFR][1000 genomes]
rs4457208	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55849324	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55889925	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56006261	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56235846	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56675463	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59308022	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs60201031	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60326618	0.86[AFR][1000 genomes]
rs6460312	0.86[AFR][1000 genomes]
rs66510832	0.83[ASN][1000 genomes]
rs67319329	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71535634	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71535635	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71563136	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs869249	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs876743	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13238612	GUSB	cis	Whole Blood	GTEx
rs13238612	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13238612	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs13238612	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs13238612	VKORC1L1	cis	Whole Blood	GTEx
rs13238612	RP4-756H11.3	cis	lung	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66310400-66337000	Weak transcription	Small Intestine	intestine
2	chr7:66311000-66339200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr7:66311000-66345800	Weak transcription	HSMMtube	muscle
4	chr7:66311000-66349400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr7:66311000-66358400	Weak transcription	Brain Anterior Caudate	brain
6	chr7:66311000-66368000	Weak transcription	Colon Smooth Muscle	Colon
7	chr7:66311000-66385200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:66311200-66343000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:66311200-66385200	Weak transcription	Brain Angular Gyrus	brain
10	chr7:66311600-66334000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:66313800-66336000	Weak transcription	HMEC	breast
12	chr7:66314400-66342800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr7:66317200-66364400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr7:66319400-66364800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr7:66321200-66367800	Weak transcription	Aorta	Aorta
16	chr7:66321800-66337400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr7:66322400-66342600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr7:66322400-66364200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr7:66324400-66363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:66325200-66334200	Weak transcription	GM12878-XiMat	blood
21	chr7:66325200-66360200	Weak transcription	Psoas Muscle	Psoas
22	chr7:66325200-66366400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr7:66325400-66351200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:66325400-66366400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:66325400-66369400	Weak transcription	Fetal Brain Female	brain
26	chr7:66325600-66334400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr7:66325600-66345200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr7:66325600-66359000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr7:66325600-66363600	Weak transcription	Primary B cells from cord blood	blood
30	chr7:66325600-66363600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr7:66325600-66373000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr7:66325800-66334800	Weak transcription	Thymus	Thymus
33	chr7:66325800-66335200	Weak transcription	Placenta	Placenta
34	chr7:66325800-66343800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:66325800-66344200	Weak transcription	Left Ventricle	heart
36	chr7:66325800-66344200	Weak transcription	Pancreas	Pancrea
37	chr7:66325800-66344400	Weak transcription	NHEK	skin
38	chr7:66325800-66350000	Weak transcription	Dnd41	blood
39	chr7:66325800-66352800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr7:66325800-66359600	Weak transcription	Spleen	Spleen
41	chr7:66325800-66363400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr7:66325800-66363400	Weak transcription	Brain Substantia Nigra	brain
43	chr7:66325800-66365800	Weak transcription	Esophagus	oesophagus
44	chr7:66325800-66366400	Weak transcription	Right Ventricle	heart
45	chr7:66325800-66367000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr7:66325800-66367600	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr7:66326000-66335200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr7:66326000-66343800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:66326000-66349600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr7:66326000-66362000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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