Variant report

Variant	rs17480344
Chromosome Location	chr1:223504688-223504689
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223504054..223506980-chr1:223508583..223510799,2	K562	blood:
2	chr1:223502794..223505270-chr1:223535922..223537884,2	MCF-7	breast:
3	chr1:223503941..223506228-chr1:223511294..223513326,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143502	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10495206	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495207	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10907376	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs11261264	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12123148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12140453	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12564615	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1400959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1547788	0.81[EUR][1000 genomes]
rs17162008	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17162072	0.92[JPT][hapmap]
rs17163827	0.85[EUR][1000 genomes]
rs17163831	0.80[EUR][1000 genomes]
rs17479856	0.83[JPT][hapmap]
rs17480087	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17518349	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17518363	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17538964	0.83[JPT][hapmap]
rs17539269	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17539583	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17577742	0.84[ASW][hapmap];0.88[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17578168	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17578203	0.84[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1772280	0.83[EUR][1000 genomes]
rs34150324	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61838208	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61838209	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61838210	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61838229	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61838230	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61838231	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61838234	0.81[EUR][1000 genomes]
rs61838235	0.81[EUR][1000 genomes]
rs61838238	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61838239	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61838240	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61838243	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61838250	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61838252	0.83[EUR][1000 genomes]
rs61839867	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7536652	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs7541162	0.81[EUR][1000 genomes]
rs9442042	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[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	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	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
3	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17480344	SUSD4	cis	cerebellum	SCAN
rs17480344	SUSD4	cis	Heart Left Ventricle	GTEx
rs17480344	SUSD4	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223497200-223512600	Weak transcription	Pancreas	Pancrea
2	chr1:223497400-223510400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:223501400-223506400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:223502200-223505000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:223502400-223504800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:223503000-223505600	Enhancers	Ovary	ovary
7	chr1:223503000-223506000	Weak transcription	Esophagus	oesophagus
8	chr1:223503800-223505800	Enhancers	Fetal Lung	lung
9	chr1:223504000-223505400	Enhancers	Aorta	Aorta
10	chr1:223504000-223506000	Enhancers	HMEC	breast
11	chr1:223504200-223505000	Enhancers	Thymus	Thymus
12	chr1:223504200-223505200	Weak transcription	Fetal Kidney	kidney
13	chr1:223504200-223505600	Enhancers	Primary T cells from cord blood	blood
14	chr1:223504200-223505600	Enhancers	Primary T cells fromperipheralblood	blood
15	chr1:223504200-223505600	Enhancers	Right Atrium	heart
16	chr1:223504200-223506600	Enhancers	Fetal Thymus	thymus
17	chr1:223504400-223505600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr1:223504400-223505600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr1:223504400-223506000	Enhancers	NHEK	skin
20	chr1:223504400-223506800	Enhancers	Fetal Heart	heart
21	chr1:223504400-223507000	Weak transcription	Brain Anterior Caudate	brain
22	chr1:223504600-223505400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:223504600-223505400	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr1:223504600-223505600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:223504600-223505600	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr1:223504600-223505800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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