Variant report

Variant	rs12122451
Chromosome Location	chr1:223351786-223351787
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr1:223350983-223352011	HEK293-T-REx	kidney:	n/a	chr1:223351790-223351799 chr1:223351782-223351803

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223348196..223351831-chr1:223853498..223856683,4	MCF-7	breast:
2	chr1:223351680..223354342-chr1:223666424..223669098,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226601	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1341986	0.96[ASN][1000 genomes]
rs1640827	0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17609948	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17661703	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1773750	0.94[ASN][1000 genomes]
rs1773755	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1773756	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1773757	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1773758	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2247421	0.84[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2487835	0.94[ASN][1000 genomes]
rs4140967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61837564	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61837568	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61837569	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61837573	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61837574	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61837575	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61837576	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61837577	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs67947164	0.84[AMR][1000 genomes]
rs72743863	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72743865	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72743873	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72743881	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs851166	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs851171	0.95[CEU][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs851191	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs975089	0.93[AMR][1000 genomes];0.94[EUR][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	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	nsv832659	chr1:223294767-223438487	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12122451	SUSD4	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223347800-223357600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:223348600-223352200	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:223348600-223352200	Weak transcription	Brain Substantia Nigra	brain
4	chr1:223348800-223352400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:223348800-223355400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr1:223349600-223355000	Enhancers	Adipose Nuclei	Adipose
7	chr1:223349600-223355000	Enhancers	Placenta	Placenta
8	chr1:223349800-223375400	Weak transcription	Right Atrium	heart
9	chr1:223350000-223352600	Enhancers	Fetal Muscle Leg	muscle
10	chr1:223350000-223355800	Enhancers	Fetal Thymus	thymus
11	chr1:223350200-223355400	Enhancers	Liver	Liver
12	chr1:223350400-223352000	Enhancers	Lung	lung
13	chr1:223350600-223353000	Weak transcription	Brain Anterior Caudate	brain
14	chr1:223350800-223353400	Enhancers	Pancreas	Pancrea
15	chr1:223351000-223351800	Enhancers	Stomach Mucosa	stomach
16	chr1:223351000-223351800	Enhancers	K562	blood
17	chr1:223351000-223352200	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr1:223351000-223352600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:223351200-223351800	Enhancers	HepG2	liver
20	chr1:223351200-223352000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:223351400-223351800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr1:223351400-223351800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:223351400-223352000	Enhancers	Primary B cells from cord blood	blood
24	chr1:223351400-223352200	Enhancers	Primary hematopoietic stem cells	blood
25	chr1:223351600-223351800	Flanking Active TSS	Esophagus	oesophagus

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