Variant report

Variant	rs4683335
Chromosome Location	chr3:42855765-42855766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42842006..42848504-chr3:42854036..42858354,7	K562	blood:
2	chr3:42846757..42848695-chr3:42854131..42856830,2	K562	blood:
3	chr3:42841845..42845236-chr3:42855285..42858253,3	K562	blood:
4	chr3:42853502..42856729-chr3:42859080..42861862,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181061	Chromatin interaction
ENSG00000144648	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11129975	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11129976	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11129977	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11922832	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12491179	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs12639142	0.95[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs13070029	0.97[EUR][1000 genomes]
rs13096498	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2372110	0.92[EUR][1000 genomes]
rs339671	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs339684	0.87[CEU][hapmap]
rs339731	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs34868846	0.97[EUR][1000 genomes]
rs35584330	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3843369	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3846063	0.95[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs4683332	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6442067	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6779561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7641046	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1847016	chr3:42855765-42880490	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4683335	CCDC13	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42846800-42856400	Weak transcription	Right Atrium	heart
2	chr3:42847200-42856400	Weak transcription	NHEK	skin
3	chr3:42847400-42856200	Weak transcription	Colonic Mucosa	Colon
4	chr3:42849800-42856400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:42853200-42856200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:42853200-42856600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:42853200-42858600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr3:42853600-42856000	Weak transcription	Stomach Mucosa	stomach
9	chr3:42853600-42856400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:42853800-42855800	Weak transcription	HepG2	liver
11	chr3:42853800-42856400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:42853800-42861000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:42853800-42861200	Weak transcription	Fetal Intestine Large	intestine
14	chr3:42853800-42862200	Weak transcription	Fetal Intestine Small	intestine
15	chr3:42854000-42856600	Weak transcription	Fetal Kidney	kidney
16	chr3:42854200-42856200	Weak transcription	Placenta	Placenta
17	chr3:42854200-42861200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:42854800-42858000	Enhancers	Fetal Heart	heart
19	chr3:42855000-42855800	ZNF genes & repeats	K562	blood
20	chr3:42855000-42857600	Enhancers	Placenta Amnion	Placenta Amnion
21	chr3:42855600-42856400	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr3:42855600-42857400	Enhancers	Rectal Mucosa Donor 29	rectum

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