Variant report

Variant	rs2252567
Chromosome Location	chr8:11660916-11660917
allele	C/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	JUND	chr8:11659738-11661067	K562	blood:	n/a	chr8:11660198-11660207 chr8:11660117-11660126
2	ZNF143	chr8:11659844-11661001	Hela-S3	cervix:	n/a	chr8:11660636-11660646 chr8:11660761-11660776
3	HCFC1	chr8:11659437-11661136	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr8:11659473-11661258	K562	blood:	n/a	n/a
5	POLR2A	chr8:11660565-11661100	HepG2	liver:	n/a	n/a
6	GATA3	chr8:11660516-11661094	T-47D	breast:	n/a	chr8:11660827-11660836 chr8:11661051-11661061 chr8:11661052-11661061
7	POLR2A	chr8:11659699-11660940	HepG2	liver:	n/a	n/a
8	POLR2A	chr8:11659602-11660928	MCF-7	breast:	n/a	n/a
9	ARID3A	chr8:11660655-11661419	K562	blood:	n/a	n/a
10	MAZ	chr8:11659492-11661341	IMR90	lung:	n/a	chr8:11659821-11659832 chr8:11659824-11659833 chr8:11659821-11659831
11	POLR2A	chr8:11659352-11660997	GM18505	blood:	n/a	n/a
12	RELA	chr8:11659637-11661100	GM15510	blood:	n/a	n/a
13	POLR2A	chr8:11659417-11661294	GM18951	blood:	n/a	n/a
14	MAX	chr8:11659548-11661745	Hela-S3	cervix:	n/a	chr8:11659821-11659832 chr8:11661370-11661381 chr8:11659824-11659833 chr8:11659821-11659831
15	USF2	chr8:11660760-11660942	GM12878	blood:	n/a	n/a
16	GATA1	chr8:11659383-11661536	K562	blood:	n/a	chr8:11660827-11660836 chr8:11661051-11661061 chr8:11661052-11661061
17	POLR2A	chr8:11659556-11660926	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr8:11660071-11660919	GM12878	blood:	n/a	n/a
19	CHD2	chr8:11659647-11660934	Hela-S3	cervix:	n/a	n/a
20	TEAD4	chr8:11659411-11661349	K562	blood:	n/a	chr8:11659549-11659558
21	CREB1	chr8:11659357-11660952	HepG2	liver:	n/a	n/a
22	CEBPD	chr8:11660621-11661150	K562	blood:	n/a	n/a
23	SMARCB1	chr8:11659647-11660937	Hela-S3	cervix:	n/a	n/a
24	GATA3	chr8:11660676-11661001	MCF-7	breast:	n/a	chr8:11660827-11660836
25	E2F6	chr8:11659374-11661028	K562	blood:	n/a	chr8:11660465-11660477 chr8:11660199-11660208 chr8:11660190-11660199 chr8:11660115-11660124 chr8:11660636-11660646 chr8:11660081-11660090
26	RCOR1	chr8:11659580-11661038	Hela-S3	cervix:	n/a	n/a
27	GATA2	chr8:11660449-11661032	K562	blood:	n/a	chr8:11660826-11660840 chr8:11660827-11660836
28	ZNF263	chr8:11660204-11661223	HEK293-T-REx	kidney:	n/a	n/a
29	POLR2A	chr8:11657712-11662103	GM12891	blood:	n/a	n/a
30	HEY1	chr8:11659081-11661457	HepG2	liver:	n/a	chr8:11660159-11660174
31	TAF1	chr8:11660580-11661094	PFSK-1	brain:	n/a	n/a
32	TBP	chr8:11660689-11661471	Hela-S3	cervix:	n/a	n/a
33	E2F4	chr8:11660661-11661028	MCF10A-Er-Src	breast:	n/a	n/a
34	USF2	chr8:11660696-11661267	Hela-S3	cervix:	n/a	n/a
35	RCOR1	chr8:11659747-11661031	K562	blood:	n/a	n/a
36	MXI1	chr8:11659588-11662078	GM12878	blood:	n/a	chr8:11659821-11659830
37	STAT3	chr8:11660662-11660947	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr8:11659001-11660992	ECC-1	luminal epithelium:	n/a	n/a
39	MAX	chr8:11659575-11661435	ECC-1	luminal epithelium:	n/a	chr8:11659821-11659832 chr8:11661370-11661381 chr8:11659824-11659833 chr8:11659821-11659831
40	MYC	chr8:11659551-11661380	NB4	blood:	n/a	chr8:11659821-11659832 chr8:11659824-11659833 chr8:11659821-11659831
41	TAF1	chr8:11660669-11660940	K562	blood:	n/a	n/a
42	KAP1	chr8:11660818-11661297	U2OS	brain:	n/a	n/a
43	POLR2A	chr8:11659449-11660975	H1-neurons	neurons:	n/a	n/a
44	CEBPB	chr8:11659832-11661066	Hela-S3	cervix:	n/a	n/a
45	MAX	chr8:11660516-11661004	K562	blood:	n/a	n/a
46	UBTF	chr8:11659699-11661339	K562	blood:	n/a	n/a
47	UBTF	chr8:11659603-11661322	K562	blood:	n/a	n/a
48	POLR2A	chr8:11659388-11660969	NB4	blood:	n/a	n/a
49	POLR2A	chr8:11659543-11660968	GM18526	blood:	n/a	n/a
50	SRF	chr8:11659751-11661013	ECC-1	luminal epithelium:	n/a	chr8:11660194-11660204

No.	Distal block	Cell Line	Cell type
1	chr8:11645433..11648215-chr8:11658187..11661640,5	MCF-7	breast:
2	chr8:11660132..11662159-chr8:11687088..11688698,2	MCF-7	breast:
3	chr8:11658864..11661745-chr8:11724576..11726431,3	MCF-7	breast:
4	chr8:11658229..11662389-chr8:11662980..11669380,10	MCF-7	breast:
5	chr8:11652587..11657894-chr8:11658127..11661459,7	K562	blood:
6	chr8:11659426..11661474-chr8:11724613..11726870,3	MCF-7	breast:
7	chr8:11625747..11629309-chr8:11658765..11661345,4	K562	blood:
8	chr8:11658127..11661675-chr8:11664375..11667732,3	K562	blood:
9	chr8:11626596..11628658-chr8:11659514..11662088,3	K562	blood:
10	chr8:11624784..11628111-chr8:11660073..11663416,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NEIL2-2	chr8:11660814-11661009	NONHSAT125087

Variant related genes	Relation type
FDFT1	TF binding region
ENSG00000255046	TF binding region
ENSG00000079459	Chromatin interaction
ENSG00000227203	Chromatin interaction
ENSG00000164733	Chromatin interaction
ENSG00000154328	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1497042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1616534	0.81[AMR][1000 genomes]
rs1736057	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1736060	0.85[ASN][1000 genomes]
rs2645429	0.84[ASN][1000 genomes]
rs2645430	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2686197	0.81[ASN][1000 genomes]
rs3824114	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv1023803	chr8:11623570-11721655	Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv539476	chr8:11623570-11721655	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv890361	chr8:11625808-11755513	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv890362	chr8:11625808-11771089	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv1032739	chr8:11643803-11716473	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv890363	chr8:11647941-11681825	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv890364	chr8:11654796-11671041	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv1034132	chr8:11657033-12198242	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2252567	FDFT1	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11658400-11666800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr8:11659000-11663400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr8:11659200-11661200	Active TSS	Brain Hippocampus Middle	brain
4	chr8:11659200-11663200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr8:11659400-11661000	Active TSS	Fetal Kidney	kidney
6	chr8:11659400-11661200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr8:11659400-11661200	Active TSS	Right Ventricle	heart
8	chr8:11659400-11661400	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr8:11659400-11661400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr8:11659400-11661400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr8:11659400-11661600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr8:11659400-11661600	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr8:11659400-11661800	Active TSS	A549	lung
14	chr8:11659400-11662600	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr8:11659400-11663800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr8:11659600-11661000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:11659600-11661000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr8:11659600-11661000	Active TSS	Colon Smooth Muscle	Colon
19	chr8:11659600-11661000	Active TSS	Fetal Heart	heart
20	chr8:11659600-11661000	Active TSS	Fetal Lung	lung
21	chr8:11659600-11661000	Active TSS	Placenta Amnion	Placenta Amnion
22	chr8:11659600-11661200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr8:11659600-11661200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
24	chr8:11659600-11661200	Active TSS	Left Ventricle	heart
25	chr8:11659600-11661200	Active TSS	Psoas Muscle	Psoas
26	chr8:11659600-11661200	Active TSS	Rectal Smooth Muscle	rectum
27	chr8:11659600-11661400	Active TSS	Aorta	Aorta
28	chr8:11659600-11661400	Active TSS	Gastric	stomach
29	chr8:11659600-11661600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr8:11659600-11661600	Active TSS	Brain Angular Gyrus	brain
31	chr8:11659600-11661600	Active TSS	Right Atrium	heart
32	chr8:11659600-11661600	Active TSS	Hela-S3	cervix
33	chr8:11659600-11662000	Active TSS	Ovary	ovary
34	chr8:11659600-11662000	Active TSS	HSMM	muscle
35	chr8:11659600-11662200	Active TSS	Brain Cingulate Gyrus	brain
36	chr8:11659600-11662200	Active TSS	Esophagus	oesophagus
37	chr8:11659600-11662400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr8:11659600-11662400	Active TSS	Small Intestine	intestine
39	chr8:11659600-11662600	Active TSS	H1 Cell Line	embryonic stem cell
40	chr8:11659600-11662600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr8:11659600-11663000	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr8:11659600-11663200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr8:11659600-11663200	Active TSS	Fetal Brain Female	brain
44	chr8:11659600-11663400	Active TSS	Fetal Brain Male	brain
45	chr8:11659600-11663400	Active TSS	NHLF	lung
46	chr8:11659600-11663600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr8:11659600-11664200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr8:11659600-11664200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr8:11659800-11661000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr8:11659800-11661000	Active TSS	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links