Variant report

Variant	rs2296565
Chromosome Location	chr14:67879037-67879038
allele	A/G
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	E2F1	chr14:67878553-67879123	Hela-S3	cervix:	n/a	n/a
2	BRCA1	chr14:67878786-67879074	Hela-S3	cervix:	n/a	n/a
3	TCF12	chr14:67878379-67879290	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr14:67878579-67879342	HCT-116	colon:	n/a	n/a
5	MAX	chr14:67878346-67879407	ECC-1	luminal epithelium:	n/a	chr14:67879360-67879370
6	SMC3	chr14:67878223-67879285	Hela-S3	cervix:	n/a	n/a
7	MAX	chr14:67878287-67879373	A549	lung:	n/a	chr14:67879360-67879370
8	POLR2A	chr14:67878624-67879288	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr14:67878641-67879247	MCF10A-Er-Src	breast:	n/a	n/a
10	E2F4	chr14:67878719-67879148	MCF10A-Er-Src	breast:	n/a	n/a
11	E2F6	chr14:67878528-67879313	H1-hESC	embryonic stem cell:	n/a	chr14:67879182-67879193
12	FOS	chr14:67878901-67879079	MCF10A-Er-Src	breast:	n/a	n/a
13	MAX	chr14:67878424-67879383	MCF-7	breast:	n/a	chr14:67879360-67879370
14	TCF7L2	chr14:67878552-67879353	HCT-116	colon:	n/a	n/a
15	ELK1	chr14:67878769-67879115	Hela-S3	cervix:	n/a	n/a
16	MAX	chr14:67878475-67879283	H1-hESC	embryonic stem cell:	n/a	n/a
17	STAT3	chr14:67879025-67879151	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr14:67878465-67879332	HCT-116	colon:	n/a	n/a
19	MAX	chr14:67878292-67879450	HCT-116	colon:	n/a	chr14:67879360-67879370
20	MAZ	chr14:67878559-67879309	Hela-S3	cervix:	n/a	n/a
21	TCF7L2	chr14:67878681-67879147	Hela-S3	cervix:	n/a	n/a
22	TFAP2A	chr14:67878588-67879327	Hela-S3	cervix:	n/a	chr14:67878934-67878942 chr14:67878935-67878943 chr14:67878922-67878937 chr14:67878926-67878936 chr14:67878933-67878944 chr14:67878934-67878942 chr14:67878926-67878936 chr14:67878926-67878936 chr14:67878935-67878943 chr14:67878933-67878944 chr14:67878935-67878943 chr14:67878933-67878944 chr14:67878924-67878938 chr14:67878926-67878938 chr14:67878934-67878942
23	E2F6	chr14:67878403-67879355	H1-hESC	embryonic stem cell:	n/a	chr14:67879182-67879193
24	HA-E2F1	chr14:67878092-67879396	MCF-7	breast:	n/a	chr14:67879182-67879193
25	MAX	chr14:67878557-67879201	A549	lung:	n/a	n/a
26	MAX	chr14:67878499-67879212	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr14:67877942-67879240	PBDE	blood:	n/a	n/a
28	E2F6	chr14:67878614-67879289	A549	lung:	n/a	chr14:67879182-67879193
29	POLR2A	chr14:67878474-67879204	MCF-7	breast:	n/a	n/a
30	POLR2A	chr14:67878604-67879183	HCT-116	colon:	n/a	n/a
31	ZKSCAN1	chr14:67878710-67879063	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr14:67878607-67879258	Hela-S3	cervix:	n/a	n/a
33	RCOR1	chr14:67878547-67879232	Hela-S3	cervix:	n/a	n/a
34	HA-E2F1	chr14:67878447-67879164	Hela-S3	cervix:	n/a	n/a
35	MAX	chr14:67878403-67879368	HCT-116	colon:	n/a	n/a
36	POLR2A	chr14:67878551-67879299	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr14:67878513-67879108	MCF-7	breast:	n/a	n/a
38	E2F6	chr14:67878374-67879395	A549	lung:	n/a	chr14:67879182-67879193
39	CEBPB	chr14:67878603-67879265	Hela-S3	cervix:	n/a	n/a
40	RFX5	chr14:67878765-67879145	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr14:67877944-67879325	Hela-S3	cervix:	n/a	n/a
42	MYC	chr14:67878619-67879271	MCF10A-Er-Src	breast:	n/a	n/a
43	MYC	chr14:67878489-67879101	MCF-7	breast:	n/a	n/a
44	CREB1	chr14:67878586-67879108	A549	lung:	n/a	n/a
45	POLR2A	chr14:67879034-67879062	ProgFib	skin:	n/a	n/a
46	NFYA	chr14:67878752-67879229	Hela-S3	cervix:	n/a	n/a
47	SMARCB1	chr14:67877964-67879358	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr14:67878587-67879133	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr14:67878512-67879230	Hela-S3	cervix:	n/a	n/a
50	MXI1	chr14:67878607-67879075	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:67878492..67879251-chr2:85765787..85766682,2	Hela-S3	cervix:
2	chr12:7052685..7053680-chr14:67878710..67879228,2	Hela-S3	cervix:
3	chr14:67878348..67879211-chr15:34659300..34659943,2	Hela-S3	cervix:

Variant related genes	Relation type
PLEK2	TF binding region
ENSG00000168906	Chromatin interaction
ENSG00000238923	Chromatin interaction
ENSG00000176454	Chromatin interaction
ENSG00000111678	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1290900	0.83[MEX][hapmap]
rs7141756	0.83[ASW][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.81[LWK][hapmap]
rs8011893	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2296565	FAM71D	cis	cerebellum	SCAN
rs2296565	EIF2S1	cis	lymphoblastoid	seeQTL
rs2296565	ATP6V1D	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:67877800-67879600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr14:67877800-67880200	Weak transcription	K562	blood
3	chr14:67878000-67879200	Active TSS	Esophagus	oesophagus
4	chr14:67878000-67879200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
5	chr14:67878000-67879200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
6	chr14:67878000-67879400	Flanking Active TSS	Pancreas	Pancrea
7	chr14:67878200-67879200	Active TSS	Fetal Intestine Small	intestine
8	chr14:67878200-67879200	Active TSS	Gastric	stomach
9	chr14:67878200-67879200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
10	chr14:67878200-67879200	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
11	chr14:67878200-67879200	Active TSS	Stomach Mucosa	stomach
12	chr14:67878200-67879200	Active TSS	A549	lung
13	chr14:67878200-67879200	Active TSS	NHEK	skin
14	chr14:67878200-67879400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr14:67878200-67879400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr14:67878400-67879200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr14:67878400-67879200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr14:67878400-67879200	Active TSS	H9 Cell Line	embryonic stem cell
19	chr14:67878400-67879200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
20	chr14:67878400-67879200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
21	chr14:67878400-67879200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
22	chr14:67878400-67879200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr14:67878400-67879200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr14:67878400-67879200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr14:67878400-67879200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
26	chr14:67878400-67879200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
27	chr14:67878400-67879200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr14:67878400-67879200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr14:67878400-67879200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr14:67878400-67879200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr14:67878400-67879200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
32	chr14:67878400-67879200	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr14:67878400-67879200	Flanking Active TSS	HUVEC	blood vessel
34	chr14:67878400-67879200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
35	chr14:67878400-67879200	Active TSS	NHLF	lung
36	chr14:67878400-67879400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
37	chr14:67878400-67879400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
38	chr14:67878400-67879400	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr14:67878400-67879600	Active TSS	Primary T cells from cord blood	blood
40	chr14:67878400-67879600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr14:67878400-67879600	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr14:67878600-67879200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr14:67878600-67879200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr14:67878600-67879200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr14:67878600-67879200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
46	chr14:67878600-67879200	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr14:67878600-67879200	Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr14:67878600-67879200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr14:67878600-67879200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr14:67878600-67879200	Bivalent/Poised TSS	Brain Angular Gyrus	brain

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