Variant report

Variant	rs4683332
Chromosome Location	chr3:42827437-42827438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42821893..42823608-chr3:42825720..42828571,2	K562	blood:
2	chr3:42825788..42828570-chr3:42866080..42867830,2	K562	blood:
3	chr3:42823433..42825988-chr3:42826908..42830376,3	MCF-7	breast:
4	chr3:42827288..42829555-chr3:42832078..42833794,2	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11129975	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11129976	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11129977	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11922832	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491179	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs12639142	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13070029	0.92[EUR][1000 genomes]
rs13096498	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2372110	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs339671	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs339684	0.87[CEU][hapmap]
rs339731	0.91[CEU][hapmap];0.81[GIH][hapmap];0.88[EUR][1000 genomes]
rs34868846	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35584330	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3843369	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3846063	0.96[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs4683335	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	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779561	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7641046	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[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	esv1846968	chr3:42787469-42832979	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv236207	chr3:42825586-42829088	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4683332	CCDC13	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42814800-42840800	Weak transcription	Spleen	Spleen
2	chr3:42815000-42834800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:42815200-42828200	Weak transcription	Fetal Intestine Small	intestine
4	chr3:42815200-42834800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:42815200-42834800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:42815200-42834800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:42815200-42834800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:42815200-42834800	Weak transcription	Fetal Muscle Leg	muscle
9	chr3:42815200-42834800	Weak transcription	Ovary	ovary
10	chr3:42815200-42834800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:42815200-42834800	Weak transcription	A549	lung
12	chr3:42815200-42835200	Weak transcription	Right Ventricle	heart
13	chr3:42815200-42836400	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:42815200-42837400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:42815200-42842000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:42815200-42842200	Weak transcription	Aorta	Aorta
17	chr3:42815200-42842400	Weak transcription	Psoas Muscle	Psoas
18	chr3:42815400-42827600	Weak transcription	Primary B cells from cord blood	blood
19	chr3:42815400-42832400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:42815400-42833600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:42815400-42834400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:42815400-42834800	Weak transcription	Brain Germinal Matrix	brain
23	chr3:42815400-42837200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:42815400-42844000	Weak transcription	NHDF-Ad	bronchial
25	chr3:42815600-42827600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:42815600-42841800	Weak transcription	Thymus	Thymus
27	chr3:42815600-42842000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:42815600-42842000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:42816200-42837600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:42820400-42834800	Weak transcription	HSMMtube	muscle
31	chr3:42821400-42828400	Strong transcription	Dnd41	blood
32	chr3:42821400-42837400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:42821800-42834800	Weak transcription	Esophagus	oesophagus
34	chr3:42821800-42834800	Weak transcription	Pancreas	Pancrea
35	chr3:42822000-42841200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr3:42822400-42834800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:42822400-42834800	Weak transcription	NHLF	lung
38	chr3:42822400-42837200	Weak transcription	Brain Angular Gyrus	brain
39	chr3:42822400-42843400	Weak transcription	Small Intestine	intestine
40	chr3:42822800-42827600	Weak transcription	Stomach Mucosa	stomach
41	chr3:42822800-42830000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:42822800-42834800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:42822800-42837000	Weak transcription	Brain Anterior Caudate	brain
44	chr3:42822800-42841600	Weak transcription	Brain Substantia Nigra	brain
45	chr3:42822800-42842800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr3:42822800-42844000	Weak transcription	Fetal Kidney	kidney
47	chr3:42822800-42844200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr3:42823000-42827800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr3:42823000-42832400	Weak transcription	Fetal Heart	heart
50	chr3:42823000-42842800	Weak transcription	Fetal Brain Male	brain

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