Variant report

Variant	rs9874259
Chromosome Location	chr3:142889135-142889136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:142887670..142889227-chr3:142893884..142896662,2	K562	blood:
2	chr3:142882417..142885348-chr3:142887165..142889309,2	K562	blood:

Variant related genes	Relation type
ENSG00000244171	Chromatin interaction
ENSG00000211483	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13075966	0.92[ASN][1000 genomes]
rs1545423	0.89[CHB][hapmap];0.80[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1968653	0.91[ASN][1000 genomes]
rs2352734	0.92[ASN][1000 genomes]
rs4428143	0.92[ASN][1000 genomes]
rs4440094	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4683753	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6777051	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7630393	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7643860	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7646486	0.84[CHB][hapmap]
rs894177	0.94[CHB][hapmap]
rs9813403	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1007164	chr3:142837004-142891719	Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv508250	chr3:142842454-142943722	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv34280	chr3:142887460-142962075	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9874259	TFDP2	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142882000-142891600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:142882400-142889600	Enhancers	Fetal Thymus	thymus
3	chr3:142882800-142889200	Weak transcription	Fetal Stomach	stomach
4	chr3:142884000-142891600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:142884200-142891200	Enhancers	K562	blood
6	chr3:142884600-142889400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:142884800-142889400	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr3:142885600-142890200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:142886200-142889200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr3:142886200-142889400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr3:142886200-142889800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr3:142886400-142889200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr3:142886400-142889800	Enhancers	Primary hematopoietic stem cells	blood
14	chr3:142886600-142889200	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr3:142886600-142889200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:142886600-142890400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr3:142886800-142890400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:142886800-142891400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:142887400-142889200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:142887600-142889200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:142887600-142889200	Enhancers	Thymus	Thymus
22	chr3:142887600-142889400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:142887600-142889400	Weak transcription	HSMM	muscle
24	chr3:142887600-142889600	Weak transcription	NHDF-Ad	bronchial
25	chr3:142887600-142891400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:142887800-142889200	Weak transcription	NHLF	lung
27	chr3:142887800-142889400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:142887800-142889400	Weak transcription	Hela-S3	cervix
29	chr3:142887800-142889400	Weak transcription	NHEK	skin
30	chr3:142887800-142891400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:142887800-142891800	Enhancers	Primary B cells from cord blood	blood
32	chr3:142888000-142889200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:142888000-142889400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr3:142888000-142889400	Weak transcription	HUVEC	blood vessel
35	chr3:142888000-142891200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr3:142888200-142889800	Enhancers	Spleen	Spleen
37	chr3:142888200-142891400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:142888200-142891800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:142888400-142890200	Flanking Active TSS	Dnd41	blood
40	chr3:142888600-142889400	Enhancers	GM12878-XiMat	blood
41	chr3:142888600-142890000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr3:142888600-142891600	Flanking Active TSS	Primary T cells from cord blood	blood
43	chr3:142888600-142891800	Enhancers	Primary B cells from peripheral blood	blood
44	chr3:142888800-142889200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr3:142889000-142889400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:142889000-142889600	Enhancers	Fetal Muscle Trunk	muscle
47	chr3:142889000-142890200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr3:142889000-142890200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr3:142889000-142890200	Flanking Active TSS	Fetal Lung	lung
50	chr3:142889000-142890400	Enhancers	HMEC	breast

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