Variant report

Variant	rs10498472
Chromosome Location	chr14:55354869-55354870
allele	G/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	MXI1	chr14:55354638-55355333	SK-N-SH	brain:	n/a	chr14:55354906-55354921
2	SIN3A	chr14:55354845-55355186	H1-hESC	embryonic stem cell:	n/a	chr14:55354951-55354959
3	FOXA1	chr14:55354844-55355313	HepG2	liver:	n/a	n/a
4	SIN3AK20	chr14:55354853-55355138	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:55354060..55356270-chr14:55359922..55362227,2	K562	blood:
2	chr14:55349065..55350760-chr14:55354451..55355964,2	K562	blood:
3	chr14:55351951..55354870-chr14:55368126..55370512,5	MCF-7	breast:

Variant related genes	Relation type
FDPSP3	TF binding region
ENSG00000131979	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17253577	0.91[CEU][hapmap]
rs17253591	0.91[CEU][hapmap]
rs17671345	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs17832263	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2334299	0.88[AMR][1000 genomes]
rs2878169	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs61741224	0.88[AMR][1000 genomes]
rs7156475	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[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	nsv530042	chr14:55208170-55386966	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv932970	chr14:55326559-55532749	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10498472	WDHD1	Cis_1M	lymphoblastoid	RTeQTL
rs10498472	PYGL	cis	cerebellum	SCAN
rs10498472	EXOC5	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55345400-55368200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:55348000-55355000	Weak transcription	Small Intestine	intestine
3	chr14:55348400-55356000	Weak transcription	Lung	lung
4	chr14:55348400-55368200	Weak transcription	Gastric	stomach
5	chr14:55349000-55355000	Weak transcription	K562	blood
6	chr14:55349000-55366400	Weak transcription	Hela-S3	cervix
7	chr14:55349200-55357800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr14:55349200-55358400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr14:55349200-55367400	Weak transcription	Fetal Intestine Large	intestine
10	chr14:55349200-55367400	Weak transcription	Thymus	Thymus
11	chr14:55349400-55355000	Weak transcription	Fetal Kidney	kidney
12	chr14:55349400-55356400	Weak transcription	Fetal Intestine Small	intestine
13	chr14:55349400-55367800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr14:55349600-55355800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr14:55349600-55355800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr14:55349600-55355800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr14:55349600-55367200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr14:55349600-55368000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr14:55349800-55355000	Weak transcription	Fetal Lung	lung
20	chr14:55350000-55366400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr14:55351000-55356000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr14:55352200-55355800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr14:55352400-55355800	Weak transcription	Spleen	Spleen
24	chr14:55352400-55356000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr14:55352800-55355000	Weak transcription	Liver	Liver
26	chr14:55352800-55358200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr14:55353000-55355600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr14:55353600-55365800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr14:55353800-55355600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr14:55353800-55356000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr14:55353800-55357600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr14:55353800-55358200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr14:55354000-55367200	Weak transcription	Primary T cells from cord blood	blood
34	chr14:55354200-55355000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr14:55354200-55355000	Weak transcription	GM12878-XiMat	blood
36	chr14:55354200-55357200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr14:55354600-55355200	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr14:55354600-55355400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr14:55354600-55356400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr14:55354600-55357000	Enhancers	NHEK	skin
41	chr14:55354800-55355000	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr14:55354800-55355000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr14:55354800-55355200	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr14:55354800-55355200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr14:55354800-55355200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr14:55354800-55355200	Enhancers	Esophagus	oesophagus
47	chr14:55354800-55355200	Enhancers	HMEC	breast
48	chr14:55354800-55355400	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr14:55354800-55355600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr14:55354800-55355800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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