Variant report

Variant	rs17248895
Chromosome Location	chr14:67883624-67883625
allele	A/C
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	SPI1	chr14:67883603-67883918	GM12891	blood:	n/a	n/a
2	ZKSCAN1	chr14:67883501-67883736	Hela-S3	cervix:	n/a	n/a
3	GATA1	chr14:67882529-67883772	PBDE	blood:	n/a	chr14:67883243-67883253 chr14:67882902-67882911
4	FOXA1	chr14:67883312-67883629	HepG2	liver:	n/a	chr14:67883492-67883504
5	SPI1	chr14:67883606-67883940	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:67882986..67884493-chr14:67884717..67887136,2	K562	blood:
2	chr14:67883599..67885949-chr14:67998710..68001599,3	MCF-7	breast:
3	chr14:67854344..67856660-chr14:67881111..67883754,2	K562	blood:
4	chr14:67883319..67885734-chr14:67982122..67985064,2	K562	blood:

Variant related genes	Relation type
PLEK2	TF binding region
ENSG00000198133	Chromatin interaction
ENSG00000054690	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10131212	0.83[CHD][hapmap]
rs10132093	0.81[JPT][hapmap]
rs10137094	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10137557	0.81[JPT][hapmap]
rs10138755	0.80[JPT][hapmap]
rs10138824	0.83[CHD][hapmap]
rs10141879	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs10144090	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs10144401	0.81[CHD][hapmap]
rs10144417	0.81[CHD][hapmap]
rs10145586	0.82[JPT][hapmap]
rs10146663	0.81[CHD][hapmap]
rs10146722	0.81[JPT][hapmap]
rs10147852	0.83[CHD][hapmap]
rs10148070	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10150902	0.81[CHD][hapmap]
rs1045060	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs1078194	0.87[JPT][hapmap]
rs12323911	0.81[CHD][hapmap]
rs12590956	0.87[JPT][hapmap]
rs1535491	0.83[CHD][hapmap]
rs1555853	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs17248526	0.83[CHD][hapmap]
rs2031563	0.81[CHD][hapmap]
rs2146229	0.83[CHD][hapmap]
rs2146230	0.83[CHD][hapmap]
rs2296560	0.83[CHD][hapmap]
rs3759755	0.81[CHD][hapmap]
rs3818467	0.81[CHD][hapmap]
rs3818468	0.88[CHD][hapmap];0.83[JPT][hapmap]
rs4143909	0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs6573763	0.89[JPT][hapmap]
rs7152903	0.83[CHD][hapmap]
rs7156441	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs8004148	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs8004267	0.86[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs8004332	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs8004864	0.83[JPT][hapmap]
rs8007033	0.83[CHD][hapmap]
rs8007618	0.86[CHD][hapmap];0.87[JPT][hapmap]
rs8008619	0.81[CHD][hapmap]
rs8008724	0.81[CHD][hapmap]
rs8015950	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8016037	0.83[CHD][hapmap]
rs8020262	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8021730	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8021896	0.83[CHD][hapmap]
rs9323497	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751285	chr14:67364747-67886781	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1045518	chr14:67529049-67959582	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv456331	chr14:67732861-68103780	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv564961	chr14:67732861-68103780	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv470651	chr14:67732861-68113293	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv1054389	chr14:67804987-67922598	Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv542121	chr14:67804987-67922598	Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	nsv1319	chr14:67863561-67908725	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	12 gene(s)	inside rSNPs	diseases
9	esv3487440	chr14:67863754-67892047	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
10	esv3487442	chr14:67863758-67892045	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
11	nsv902066	chr14:67873128-68103780	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17248895	FAM71D	cis	cerebellum	SCAN
rs17248895	EIF2S1	Cis_1M	lymphoblastoid	RTeQTL
rs17248895	EIF2S1	cis	lymphoblastoid	seeQTL
rs17248895	EIF2S1	cis	multi-tissue	Pritchard
rs17248895	ATP6V1D	cis	lymphoblastoid	seeQTL
rs17248895	TMEM229B	cis	parietal	SCAN
rs17248895	ATP6V1D	cis	Thyroid	GTEx
rs17248895	ATP6V1D	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:67879200-67885400	Weak transcription	Gastric	stomach
2	chr14:67879200-67886600	Weak transcription	Spleen	Spleen
3	chr14:67879600-67888400	Weak transcription	Fetal Heart	heart
4	chr14:67880000-67885400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr14:67880200-67883800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr14:67880200-67885200	Enhancers	K562	blood
7	chr14:67881000-67885600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr14:67881400-67885000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr14:67881400-67885400	Enhancers	NHEK	skin
10	chr14:67881400-67885600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr14:67881400-67885600	Weak transcription	HSMM	muscle
12	chr14:67881400-67892800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr14:67881600-67885000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr14:67881600-67885200	Weak transcription	NHDF-Ad	bronchial
15	chr14:67881600-67885400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr14:67881600-67885400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr14:67881600-67885600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr14:67881800-67885000	Weak transcription	A549	lung
19	chr14:67881800-67885200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr14:67881800-67885200	Weak transcription	HUVEC	blood vessel
21	chr14:67881800-67885400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr14:67881800-67885400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr14:67881800-67885400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr14:67881800-67885400	Weak transcription	NH-A	brain
25	chr14:67881800-67885400	Weak transcription	NHLF	lung
26	chr14:67882000-67884800	Weak transcription	HMEC	breast
27	chr14:67882400-67885000	Enhancers	Hela-S3	cervix
28	chr14:67882400-67885400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr14:67882400-67887400	Enhancers	Placenta	Placenta
30	chr14:67882600-67883800	Enhancers	Pancreas	Pancrea
31	chr14:67882600-67885200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr14:67883200-67884200	Enhancers	Primary B cells from peripheral blood	blood
33	chr14:67883400-67883800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr14:67883400-67883800	Enhancers	Primary B cells from cord blood	blood
35	chr14:67883400-67885000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr14:67883400-67885200	Weak transcription	Fetal Intestine Small	intestine
37	chr14:67883600-67883800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr14:67883600-67883800	Enhancers	Esophagus	oesophagus
39	chr14:67883600-67885000	Weak transcription	Stomach Mucosa	stomach
40	chr14:67883600-67885200	Weak transcription	Fetal Intestine Large	intestine

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