Variant report

Variant	rs479359
Chromosome Location	chr1:114662870-114662871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114657959..114660485-chr1:114662733..114665313,2	K562	blood:
2	chr1:114635004..114637775-chr1:114660348..114663171,3	MCF-7	breast:
3	chr1:114661550..114663719-chr20:45985524..45987686,2	MCF-7	breast:
4	chr1:114656303..114663278-chr1:114663805..114668148,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101040	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1872478	0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs2481087	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2629811	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2629812	0.81[CEU][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2774309	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2774310	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2774311	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs552581	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs588983	0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[ASN][1000 genomes]
rs633255	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs659646	0.90[ASN][1000 genomes]
rs661871	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs676268	0.87[CEU][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs676715	0.85[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs676743	0.81[CEU][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs677635	0.86[EUR][1000 genomes]
rs964592	0.84[CHB][hapmap];0.90[ASN][1000 genomes]
rs964593	0.90[ASN][1000 genomes]
rs964594	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1849780	chr1:114577463-114663164	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2752948	chr1:114658958-114751958	Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs479359	SYCP1	cis	parietal	SCAN
rs479359	DRAM2	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114630400-114675800	Weak transcription	Pancreas	Pancrea
2	chr1:114650800-114666000	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:114655800-114683800	Weak transcription	Right Atrium	heart
4	chr1:114657600-114665600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:114657600-114665800	Weak transcription	Brain Anterior Caudate	brain
6	chr1:114658200-114666200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:114660200-114677200	Weak transcription	Fetal Brain Female	brain
8	chr1:114660800-114665600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:114661200-114663000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr1:114661400-114664000	Weak transcription	Fetal Lung	lung
11	chr1:114661400-114664800	Weak transcription	Fetal Brain Male	brain
12	chr1:114661400-114668200	Weak transcription	Brain Germinal Matrix	brain
13	chr1:114661600-114663400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:114661600-114664600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:114661600-114664600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr1:114661600-114665200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:114661600-114665200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr1:114661600-114665200	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:114661800-114664600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:114661800-114665200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:114661800-114665800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:114662000-114665200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:114662000-114665400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:114662200-114663800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:114662200-114664400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:114662200-114665000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:114662200-114665000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:114662200-114665600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:114662400-114663400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:114662400-114663400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:114662400-114663600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr1:114662800-114663000	Genic enhancers	HUES64 Cell Line	embryonic stem cell

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