Variant report

Variant	rs13233569
Chromosome Location	chr7:66402889-66402890
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66402042..66403954-chr7:66405152..66407138,2	MCF-7	breast:
2	chr7:66402496..66404175-chr7:66454564..66457521,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12698542	0.90[AFR][1000 genomes]
rs12698551	0.96[ASN][1000 genomes]
rs13228779	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13229468	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13232393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13235282	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13236129	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13237544	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs13238478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13238612	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13246227	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1573944	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1880644	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2141924	0.90[AFR][1000 genomes]
rs2178742	0.90[AFR][1000 genomes]
rs2659903	0.90[AFR][1000 genomes]
rs2707823	0.90[AFR][1000 genomes]
rs34162778	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs34314366	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34423980	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34559676	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs34785430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34816289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35043782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35111158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35315599	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs35390465	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35481333	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs35508430	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35624856	0.85[ASN][1000 genomes]
rs35676956	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs35821254	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35851021	0.85[ASN][1000 genomes]
rs35876551	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs36059333	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4457208	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55849324	0.88[ASN][1000 genomes]
rs55889925	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56006261	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56235846	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56675463	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs59308022	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs60201031	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66510832	0.80[ASN][1000 genomes]
rs67319329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71535634	0.82[ASN][1000 genomes]
rs71535635	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs71563136	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs869249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs876743	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758118	chr7:66401430-66859253	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv2759535	chr7:66401430-66859253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13233569	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs13233569	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs13233569	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13233569	GUSB	cis	Whole Blood	GTEx
rs13233569	ASL	cis	multi-tissue	Pritchard
rs13233569	RP4-756H11.3	cis	lung	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66387600-66407200	Weak transcription	NH-A	brain
2	chr7:66387600-66409800	Weak transcription	Fetal Kidney	kidney
3	chr7:66387600-66428000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:66388200-66406800	Weak transcription	NHLF	lung
5	chr7:66388400-66406800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:66388400-66406800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr7:66388600-66403600	Weak transcription	HUVEC	blood vessel
8	chr7:66388600-66403800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:66388600-66406800	Weak transcription	NHDF-Ad	bronchial
10	chr7:66389000-66406800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:66389400-66405400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr7:66390600-66403800	Weak transcription	HSMM	muscle
13	chr7:66391200-66409800	Weak transcription	Brain Germinal Matrix	brain
14	chr7:66392600-66403400	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr7:66393000-66403600	Weak transcription	HepG2	liver
16	chr7:66393000-66406600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr7:66393400-66411800	Weak transcription	Stomach Mucosa	stomach
18	chr7:66393800-66422200	Weak transcription	Fetal Heart	heart
19	chr7:66394000-66403600	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr7:66394200-66403800	Weak transcription	Hela-S3	cervix
21	chr7:66394200-66405400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr7:66394200-66408000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr7:66394400-66405400	Weak transcription	HMEC	breast
24	chr7:66394400-66405600	Weak transcription	Colonic Mucosa	Colon
25	chr7:66395000-66404000	Weak transcription	NHEK	skin
26	chr7:66395400-66404000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr7:66395400-66406800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:66395400-66406800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr7:66395600-66403600	Weak transcription	A549	lung
30	chr7:66395600-66404600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr7:66395600-66405400	Weak transcription	Right Atrium	heart
32	chr7:66395600-66407000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr7:66395800-66404000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr7:66395800-66405400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr7:66395800-66406400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr7:66395800-66406800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr7:66395800-66406800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr7:66395800-66406800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr7:66395800-66408000	Weak transcription	Esophagus	oesophagus
40	chr7:66395800-66412800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr7:66396000-66403200	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr7:66396000-66403600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr7:66396000-66403600	Weak transcription	Thymus	Thymus
44	chr7:66396000-66404000	Weak transcription	Primary B cells from cord blood	blood
45	chr7:66396000-66404000	Weak transcription	Brain Substantia Nigra	brain
46	chr7:66396000-66405400	Weak transcription	Spleen	Spleen
47	chr7:66396000-66406600	Weak transcription	Liver	Liver
48	chr7:66396000-66406600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr7:66396000-66406800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr7:66396000-66408200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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