Variant report

Variant	rs593968
Chromosome Location	chr3:119316189-119316190
allele	C/T
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	MTA3	chr3:119315827-119317029	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:119315795-119320559	GM12878	blood:	n/a	n/a
3	IKZF1	chr3:119316165-119317802	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:119316160-119317039	GM12892	blood:	n/a	n/a
5	POLR2A	chr3:119316055-119317070	GM12892	blood:	n/a	n/a
6	ATF2	chr3:119316171-119318970	GM12878	blood:	n/a	n/a
7	STAT3	chr3:119316180-119317854	GM12878	blood:	n/a	chr3:119316548-119316559
8	NFIC	chr3:119315804-119319171	GM12878	blood:	n/a	n/a
9	PML	chr3:119314495-119320501	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:119315803-119317101	GM12892	blood:	n/a	n/a
11	FOXM1	chr3:119316168-119317781	GM12878	blood:	n/a	n/a
12	GATA2	chr3:119316165-119316631	HUVEC	blood vessel:	n/a	chr3:119316479-119316489
13	RUNX3	chr3:119315732-119318846	GM12878	blood:	n/a	chr3:119316012-119316021 chr3:119316012-119316021
14	STAT5A	chr3:119316161-119316625	GM12878	blood:	n/a	chr3:119316548-119316559
15	POLR2A	chr3:119314772-119320568	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:119315801-119317086	GM12892	blood:	n/a	n/a
17	POLR2A	chr3:119315907-119320520	GM12878	blood:	n/a	n/a
18	MTA3	chr3:119315715-119320461	GM12878	blood:	n/a	n/a
19	FOXM1	chr3:119316121-119318989	GM12878	blood:	n/a	n/a
20	BCLAF1	chr3:119315811-119317043	GM12878	blood:	n/a	n/a
21	NFATC1	chr3:119316023-119317868	GM12878	blood:	n/a	n/a
22	RUNX3	chr3:119315874-119316194	GM12878	blood:	n/a	chr3:119316012-119316021 chr3:119316012-119316021
23	ATF2	chr3:119315942-119318112	GM12878	blood:	n/a	n/a
24	EBF1	chr3:119315831-119316204	GM12878	blood:	n/a	n/a
25	NFATC1	chr3:119316178-119318039	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PLA1A	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10433338	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13443	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1525838	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534154	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1723969	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1797831	0.96[ASN][1000 genomes]
rs1797832	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2049501	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs20569	0.80[EUR][1000 genomes]
rs2171025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2248483	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2251566	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272267	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272268	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272269	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272270	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2629399	0.96[ASN][1000 genomes]
rs2629400	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2629408	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2670293	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2670298	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688638	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688639	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688646	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688647	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688648	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692612	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692613	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2692614	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692615	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2692623	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474926	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs485257	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487124	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528765	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs530389	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs530783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs536624	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs538136	0.97[ASN][1000 genomes]
rs551885	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555525	1.00[ASN][1000 genomes]
rs55670246	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55801535	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56197198	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58020513	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs666134	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.95[ASN][1000 genomes]
rs6807201	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.96[ASN][1000 genomes]
rs6807613	0.94[ASN][1000 genomes]
rs72954966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv3963	chr3:119301064-119345904	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	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
rs593968	CCDC85A	trans	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119299800-119318000	Weak transcription	Fetal Heart	heart
2	chr3:119306000-119316800	Weak transcription	Pancreas	Pancrea
3	chr3:119307600-119316400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:119310600-119319800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:119311000-119317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:119311200-119316800	Weak transcription	Fetal Lung	lung
7	chr3:119314200-119317200	Enhancers	Lung	lung
8	chr3:119314400-119318600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:119314600-119316200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:119314600-119316400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr3:119314800-119316200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:119314800-119316200	Enhancers	Placenta	Placenta
13	chr3:119314800-119316800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:119314800-119317400	Enhancers	Primary B cells from peripheral blood	blood
15	chr3:119315000-119316200	Enhancers	Right Atrium	heart
16	chr3:119315000-119316200	Enhancers	Spleen	Spleen
17	chr3:119315000-119316400	Enhancers	Liver	Liver
18	chr3:119315000-119316400	Enhancers	Fetal Intestine Small	intestine
19	chr3:119315000-119316600	Enhancers	Muscle Satellite Cultured Cells	--
20	chr3:119315000-119316800	Weak transcription	Ovary	ovary
21	chr3:119315000-119316800	Enhancers	HSMM	muscle
22	chr3:119315000-119317800	Enhancers	Adipose Nuclei	Adipose
23	chr3:119315000-119318000	Enhancers	Psoas Muscle	Psoas
24	chr3:119315000-119320200	Enhancers	Left Ventricle	heart
25	chr3:119315200-119316200	Weak transcription	Stomach Mucosa	stomach
26	chr3:119315200-119316600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr3:119315200-119316600	Weak transcription	Osteobl	bone
28	chr3:119315200-119317000	Enhancers	A549	lung
29	chr3:119315200-119317000	Enhancers	HepG2	liver
30	chr3:119315200-119317000	Enhancers	HSMMtube	muscle
31	chr3:119315200-119317400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:119315400-119316400	Enhancers	Fetal Intestine Large	intestine
33	chr3:119315400-119316400	Enhancers	GM12878-XiMat	blood
34	chr3:119315400-119316600	Weak transcription	Small Intestine	intestine
35	chr3:119315400-119317600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:119315400-119319200	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr3:119315600-119316400	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr3:119315600-119316600	Weak transcription	Right Ventricle	heart
39	chr3:119315600-119317800	Weak transcription	Gastric	stomach
40	chr3:119315600-119319000	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr3:119315600-119319600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:119315800-119316200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:119316000-119316200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr3:119316000-119317200	Enhancers	HUVEC	blood vessel
45	chr3:119316000-119317400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:119316000-119319200	Weak transcription	Fetal Muscle Trunk	muscle

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