Variant report

Variant	rs56235846
Chromosome Location	chr7:66364225-66364226
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs12698542	0.85[AFR][1000 genomes]
rs12698551	0.95[ASN][1000 genomes]
rs13228779	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13229468	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13232393	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13233569	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13235282	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13236129	0.85[AFR][1000 genomes]
rs13237544	0.83[ASN][1000 genomes]
rs13238478	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13238612	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13246227	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1573944	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1882655	0.85[AFR][1000 genomes]
rs1922723	0.85[AFR][1000 genomes]
rs2141924	0.85[AFR][1000 genomes]
rs2178742	0.85[AFR][1000 genomes]
rs2659903	0.85[AFR][1000 genomes]
rs2659911	0.85[AFR][1000 genomes]
rs2659913	0.85[AFR][1000 genomes]
rs2707823	0.85[AFR][1000 genomes]
rs2707830	0.85[AFR][1000 genomes]
rs2707838	0.85[AFR][1000 genomes]
rs2707840	0.85[AFR][1000 genomes]
rs34162778	0.85[AFR][1000 genomes]
rs34314366	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34423980	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34559676	0.85[AFR][1000 genomes]
rs34785430	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34816289	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35043782	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35111158	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35315599	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs35390465	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35481333	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs35508430	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35624856	0.83[ASN][1000 genomes]
rs35676956	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs35821254	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35851021	0.83[ASN][1000 genomes]
rs36059333	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4457208	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55849324	0.86[ASN][1000 genomes]
rs55889925	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56006261	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56675463	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs59308022	0.86[ASN][1000 genomes]
rs60201031	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60326618	0.85[AFR][1000 genomes]
rs6460312	0.85[AFR][1000 genomes]
rs67319329	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71535634	0.81[ASN][1000 genomes]
rs71535635	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71563136	0.85[AFR][1000 genomes]
rs869249	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs876743	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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
rs56235846	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs56235846	RP4-756H11.3	cis	lung	GTEx
rs56235846	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs56235846	ASL	cis	multi-tissue	Pritchard
rs56235846	GUSB	cis	Whole Blood	GTEx
rs56235846	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66311000-66368000	Weak transcription	Colon Smooth Muscle	Colon
2	chr7:66311000-66385200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:66311200-66385200	Weak transcription	Brain Angular Gyrus	brain
4	chr7:66317200-66364400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr7:66319400-66364800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr7:66321200-66367800	Weak transcription	Aorta	Aorta
7	chr7:66325200-66366400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:66325400-66366400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:66325400-66369400	Weak transcription	Fetal Brain Female	brain
10	chr7:66325600-66373000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr7:66325800-66365800	Weak transcription	Esophagus	oesophagus
12	chr7:66325800-66366400	Weak transcription	Right Ventricle	heart
13	chr7:66325800-66367000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr7:66325800-66367600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr7:66326400-66368200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr7:66326400-66371800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr7:66328200-66367000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr7:66329800-66372000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr7:66330400-66366000	Weak transcription	Fetal Thymus	thymus
20	chr7:66331800-66378400	Weak transcription	A549	lung
21	chr7:66333000-66371600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr7:66333800-66371800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr7:66334200-66367600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:66335400-66371400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr7:66336200-66364600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr7:66336200-66366400	Weak transcription	Thymus	Thymus
27	chr7:66336200-66369400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr7:66342800-66370600	Weak transcription	NHLF	lung
29	chr7:66343000-66367600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr7:66344600-66368200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr7:66344800-66364400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr7:66345600-66368400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr7:66346000-66367000	Weak transcription	Fetal Intestine Large	intestine
34	chr7:66347000-66370000	Weak transcription	Colonic Mucosa	Colon
35	chr7:66348000-66368200	Weak transcription	Brain Germinal Matrix	brain
36	chr7:66349800-66368800	Weak transcription	NHEK	skin
37	chr7:66350600-66368400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr7:66350600-66385200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:66352800-66366000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr7:66353200-66379600	Weak transcription	GM12878-XiMat	blood
41	chr7:66355200-66369000	Weak transcription	Left Ventricle	heart
42	chr7:66355600-66375400	Weak transcription	Fetal Brain Male	brain
43	chr7:66356400-66371200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr7:66357800-66367600	Strong transcription	Liver	Liver
45	chr7:66358800-66371200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr7:66359200-66372800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr7:66359800-66366400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr7:66360000-66364400	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr7:66360000-66366400	Weak transcription	Spleen	Spleen
50	chr7:66360200-66366400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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