Variant report

Variant	rs4928119
Chromosome Location	chr3:99983347-99983348
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr3:99983335-99983372	GM12878	blood:	n/a	n/a
2	GATA1	chr3:99981537-99983408	PBDE	blood:	n/a	chr3:99983275-99983284

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:99979844..99981750-chr3:99981771..99983901,2	MCF-7	breast:
2	chr3:99981876..99985966-chr3:99986124..99992664,8	K562	blood:
3	chr3:99982718..99984285-chr3:100000156..100002852,2	K562	blood:
4	chr3:99614799..99616981-chr3:99982145..99984761,2	K562	blood:
5	chr3:99982526..99986006-chr3:99993690..99996529,5	K562	blood:
6	chr3:99614799..99617137-chr3:99982145..99984761,3	K562	blood:
7	chr3:99981806..99984412-chr3:100006870..100008819,2	K562	blood:

No data

Variant related genes	Relation type
TBC1D23	TF binding region
ENSG00000036054	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1036770	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10936157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11915985	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1214369	0.84[EUR][1000 genomes]
rs1214372	0.89[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs1214373	0.89[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs12696084	0.84[CEU][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs13070392	0.89[CEU][hapmap]
rs1609481	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2028494	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2029162	0.95[CHB][hapmap]
rs277636	0.88[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs277637	0.95[CHB][hapmap]
rs277652	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs277654	0.88[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs277655	0.95[CHB][hapmap];0.90[CHD][hapmap]
rs3772698	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3862050	0.81[ASN][1000 genomes]
rs4552390	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4928118	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs4928169	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62281675	0.88[EUR][1000 genomes]
rs6763594	0.88[EUR][1000 genomes]
rs6802765	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6804963	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs6808175	0.87[EUR][1000 genomes]
rs7427443	0.87[EUR][1000 genomes]
rs7618677	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs7630257	0.88[EUR][1000 genomes]
rs7637157	0.89[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs7638503	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs931332	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs967608	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9863738	0.89[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs9880795	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs9882337	0.87[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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4928119	ZNF546	trans	parietal	SCAN
rs4928119	TBC1D23	cis	Muscle Skeletal	GTEx
rs4928119	ZPLD1	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99980600-99983800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr3:99980600-99988600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:99980600-100037200	Weak transcription	Spleen	Spleen
4	chr3:99980600-100053200	Weak transcription	Gastric	stomach
5	chr3:99980800-99988800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:99981000-99983400	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr3:99981000-99983800	Weak transcription	Colonic Mucosa	Colon
8	chr3:99981000-99984400	Enhancers	Liver	Liver
9	chr3:99981000-99990400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:99981000-99996400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:99981200-99983600	Weak transcription	Stomach Mucosa	stomach
12	chr3:99981200-99984000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:99981200-99984200	Enhancers	Adipose Nuclei	Adipose
14	chr3:99981200-99985200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:99981200-99985400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:99981200-99986000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr3:99981200-99987000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:99981200-99988600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr3:99981200-99988800	Weak transcription	Fetal Brain Female	brain
20	chr3:99981200-99993200	Weak transcription	Primary B cells from cord blood	blood
21	chr3:99981200-99995400	Weak transcription	Brain Angular Gyrus	brain
22	chr3:99981200-99997800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:99981200-99998400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr3:99981200-99998600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr3:99981200-99998600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:99981200-100004800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:99981200-100030800	Weak transcription	Fetal Heart	heart
28	chr3:99981400-99986800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:99981400-99988600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:99981400-99998400	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr3:99981400-100004400	Weak transcription	Lung	lung
32	chr3:99981800-99983800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:99982000-99984200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:99982000-99984200	Enhancers	Duodenum Mucosa	Duodenum
35	chr3:99982000-99986800	Weak transcription	Right Atrium	heart
36	chr3:99982200-99983400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:99982200-99983400	Enhancers	HSMM	muscle
38	chr3:99982200-99984000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:99982200-99984200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr3:99982200-99984200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:99982200-99984200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:99982200-99984200	Enhancers	Hela-S3	cervix
43	chr3:99982200-99984200	Enhancers	HMEC	breast
44	chr3:99982200-99990400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:99982400-99984200	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr3:99982400-99984200	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr3:99982400-99984200	Flanking Active TSS	NHEK	skin
48	chr3:99982400-100005400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:99982600-99983400	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr3:99982600-99983400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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