Variant report

Variant	rs551996
Chromosome Location	chr1:225737336-225737337
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10753406	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10799311	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10799314	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10799316	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs10799317	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10799318	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10915828	0.93[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.89[YRI][hapmap]
rs10915830	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10915833	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10915834	0.92[EUR][1000 genomes]
rs10915837	0.81[ASN][1000 genomes]
rs10915839	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10915847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11584675	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12028305	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1222440	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs12729655	0.81[ASN][1000 genomes]
rs2639703	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2639712	0.81[TSI][hapmap]
rs2639716	0.84[EUR][1000 genomes]
rs2657564	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2657569	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs2840958	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2840967	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs2840968	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs3820226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3856156	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653643	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs476540	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs487591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs498350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510293	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs511649	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516249	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs554992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561656	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426076	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6668770	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6676201	0.81[ASN][1000 genomes]
rs6697783	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap]
rs6702555	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs712062	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515907	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7515963	0.81[ASN][1000 genomes]
rs7524766	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7540181	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7541598	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7555139	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7555553	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs812523	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs947034	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9804142	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs551996	LBR	cis	Artery Tibial	GTEx
rs551996	PYCR2	cis	cerebellum	SCAN
rs551996	C1orf58	cis	parietal	SCAN
rs551996	RP11-496N12.9	cis	Thyroid	GTEx
rs551996	ENAH	cis	normal skin	skin_eQTL
rs551996	DUSP10	cis	parietal	SCAN
rs551996	MIXL1	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225701400-225744400	Weak transcription	HUVEC	blood vessel
2	chr1:225701400-225747000	Weak transcription	Hela-S3	cervix
3	chr1:225705600-225747400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:225707200-225755000	Weak transcription	Gastric	stomach
5	chr1:225717600-225744400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:225717800-225744400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:225717800-225745000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:225717800-225747400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:225717800-225747400	Weak transcription	Fetal Stomach	stomach
10	chr1:225717800-225758200	Weak transcription	HepG2	liver
11	chr1:225718400-225756400	Weak transcription	NHLF	lung
12	chr1:225722800-225747600	Weak transcription	Fetal Intestine Small	intestine
13	chr1:225723200-225739600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:225726800-225744000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:225727200-225739200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:225727400-225737800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:225727400-225744400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:225727400-225747600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:225727400-225747600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:225727600-225737600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:225727600-225753600	Weak transcription	NHEK	skin
22	chr1:225728000-225753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:225728800-225737400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:225728800-225739200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:225730000-225744400	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:225730200-225737600	Weak transcription	Ovary	ovary
27	chr1:225730200-225747600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:225730200-225753400	Weak transcription	NHDF-Ad	bronchial
29	chr1:225730200-225753600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:225730400-225744000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:225730600-225737400	Weak transcription	Right Ventricle	heart
32	chr1:225730600-225747600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:225730600-225765800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:225730600-225776200	Weak transcription	Pancreas	Pancrea
35	chr1:225732000-225744400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:225732000-225744600	Weak transcription	Fetal Intestine Large	intestine
37	chr1:225732400-225737400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:225732400-225737600	Weak transcription	Psoas Muscle	Psoas
39	chr1:225732400-225763000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:225733000-225737400	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:225733000-225744400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:225733200-225737400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:225733600-225737800	Weak transcription	Brain Substantia Nigra	brain
44	chr1:225733600-225744000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:225734000-225737400	Weak transcription	Left Ventricle	heart
46	chr1:225734000-225744400	Weak transcription	Brain Angular Gyrus	brain
47	chr1:225734400-225744400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:225734600-225763600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:225734800-225737800	Weak transcription	Brain Germinal Matrix	brain
50	chr1:225735200-225740200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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