Variant report

Variant	rs17163824
Chromosome Location	chr1:223514945-223514946
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223510081..223513953-chr1:223514794..223517151,3	K562	blood:
2	chr1:223505491..223507807-chr1:223513867..223516012,2	K562	blood:
3	chr1:223496498..223499043-chr1:223513776..223516102,2	K562	blood:
4	chr1:223514593..223516719-chr1:223519953..223521559,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10495207	0.82[EUR][1000 genomes]
rs11488548	0.87[AFR][1000 genomes]
rs1547788	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1619227	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1713220	0.90[AMR][1000 genomes]
rs17162008	0.82[EUR][1000 genomes]
rs17163818	0.81[AFR][1000 genomes]
rs17163825	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17163828	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17163831	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17539583	0.84[EUR][1000 genomes]
rs17578168	0.84[EUR][1000 genomes]
rs17578203	0.84[EUR][1000 genomes]
rs2459849	0.90[AMR][1000 genomes]
rs2487521	0.90[AMR][1000 genomes]
rs2678377	0.90[AMR][1000 genomes]
rs34572097	0.81[AFR][1000 genomes]
rs35318812	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61838230	0.80[EUR][1000 genomes]
rs61838231	0.80[EUR][1000 genomes]
rs61838234	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61838235	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61838236	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61838237	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61838238	0.84[EUR][1000 genomes]
rs61838239	0.84[EUR][1000 genomes]
rs61838240	0.84[EUR][1000 genomes]
rs61838241	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61838243	0.84[EUR][1000 genomes]
rs61838246	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61838249	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61838250	0.86[EUR][1000 genomes]
rs6604709	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7536652	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7541162	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7555607	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs825127	0.81[AFR][1000 genomes]
rs825131	0.85[AFR][1000 genomes]
rs870486	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9442046	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[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	nsv1000039	chr1:223429733-223527845	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1010798	chr1:223498145-223538989	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17163824	SUSD4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223505600-223521400	Weak transcription	Primary T cells from cord blood	blood
2	chr1:223506600-223526000	Weak transcription	Esophagus	oesophagus
3	chr1:223511200-223517600	Weak transcription	Psoas Muscle	Psoas
4	chr1:223511800-223515600	Enhancers	Left Ventricle	heart
5	chr1:223511800-223515800	Enhancers	Ovary	ovary
6	chr1:223511800-223527000	Enhancers	Fetal Heart	heart
7	chr1:223512600-223515400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:223513200-223515200	Enhancers	Brain Anterior Caudate	brain
9	chr1:223513200-223517200	Weak transcription	Fetal Lung	lung
10	chr1:223513400-223515400	Enhancers	HSMMtube	muscle
11	chr1:223513600-223515200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:223513600-223515200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:223513600-223515200	Enhancers	Right Ventricle	heart
14	chr1:223513600-223515200	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr1:223513800-223515200	Enhancers	Fetal Thymus	thymus
16	chr1:223513800-223515400	Enhancers	Fetal Muscle Leg	muscle
17	chr1:223513800-223515600	Enhancers	Gastric	stomach
18	chr1:223514000-223526200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:223514200-223515000	Weak transcription	Brain Angular Gyrus	brain
20	chr1:223514200-223515200	Enhancers	Stomach Smooth Muscle	stomach
21	chr1:223514400-223515000	Weak transcription	Pancreas	Pancrea
22	chr1:223514400-223515200	Enhancers	Fetal Muscle Trunk	muscle
23	chr1:223514400-223515400	Enhancers	HSMM	muscle
24	chr1:223514400-223535800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:223514600-223516400	Weak transcription	Stomach Mucosa	stomach
26	chr1:223514800-223515200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr1:223514800-223515400	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr1:223514800-223515400	Enhancers	Right Atrium	heart

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