Variant report

Variant	rs1667619
Chromosome Location	chr2:74347576-74347577
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	RELA	chr2:74347100-74347837	GM15510	blood:	n/a	n/a
2	JUND	chr2:74347234-74347854	A549	lung:	n/a	chr2:74347733-74347742 chr2:74347339-74347348
3	POLR2A	chr2:74347221-74347868	NB4	blood:	n/a	n/a
4	EGR1	chr2:74347220-74347914	MCF-7	breast:	n/a	chr2:74347386-74347400 chr2:74347338-74347348
5	POLR2A	chr2:74347333-74347692	IMR90	lung:	n/a	n/a
6	TAF1	chr2:74347266-74347830	HepG2	liver:	n/a	n/a
7	SETDB1	chr2:74347348-74348592	U2OS	brain:	n/a	n/a
8	CHD1	chr2:74347065-74347948	GM12878	blood:	n/a	chr2:74347332-74347342
9	TCF7L2	chr2:74347435-74347674	Hela-S3	cervix:	n/a	n/a
10	TAF7	chr2:74347278-74347739	H1-hESC	embryonic stem cell:	n/a	n/a
11	SIN3AK20	chr2:74346995-74347806	SK-N-SH	brain:	n/a	n/a
12	TAF1	chr2:74347353-74347833	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:74347059-74348013	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr2:74347258-74347864	H1-neurons	neurons:	n/a	n/a
15	BHLHE40	chr2:74347357-74347932	K562	blood:	n/a	n/a
16	E2F6	chr2:74347252-74347909	Hela-S3	cervix:	n/a	chr2:74347735-74347745 chr2:74347338-74347347
17	TAF1	chr2:74347248-74347846	Hela-S3	cervix:	n/a	n/a
18	MAX	chr2:74347191-74348022	MCF-7	breast:	n/a	chr2:74347337-74347347 chr2:74347424-74347434
19	ZNF143	chr2:74347269-74347814	K562	blood:	n/a	chr2:74347337-74347347
20	MYC	chr2:74347351-74347710	K562	blood:	n/a	chr2:74347424-74347434
21	POLR2A	chr2:74347138-74347991	U87	brain:	n/a	n/a
22	TCF3	chr2:74347260-74347729	GM12878	blood:	n/a	n/a
23	POLR2A	chr2:74347096-74347979	GM12878	blood:	n/a	n/a
24	CTCF	chr2:74347224-74347877	MCF-7	breast:	n/a	chr2:74347701-74347714
25	POLR2A	chr2:74347120-74347933	PBDE	blood:	n/a	n/a
26	POLR2A	chr2:74347272-74347800	HepG2	liver:	n/a	n/a
27	CTCF	chr2:74347253-74347829	IMR90	lung:	n/a	chr2:74347701-74347714
28	CTCF	chr2:74347300-74347637	GM12891	blood:	n/a	n/a
29	GABPA	chr2:74347159-74348063	SK-N-SH	brain:	n/a	chr2:74347338-74347347
30	ELF1	chr2:74347125-74347917	HepG2	liver:	n/a	n/a
31	CTCF	chr2:74347297-74347582	MCF-7	breast:	n/a	n/a
32	POLR2A	chr2:74346970-74347962	Hela-S3	cervix:	n/a	n/a
33	REST	chr2:74347146-74347975	HL-60	blood:	n/a	chr2:74347352-74347365
34	MXI1	chr2:74347310-74348015	GM12878	blood:	n/a	n/a
35	ZC3H11A	chr2:74346713-74347930	K562	blood:	n/a	n/a
36	ZNF143	chr2:74347238-74347722	GM12878	blood:	n/a	chr2:74347337-74347347
37	CTCF	chr2:74347290-74347613	A549	lung:	n/a	n/a
38	POLR2A	chr2:74347061-74347874	K562	blood:	n/a	n/a
39	POLR2A	chr2:74347073-74347861	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr2:74347263-74347885	GM12878	blood:	n/a	n/a
41	TCF12	chr2:74347118-74348053	A549	lung:	n/a	n/a
42	HA-E2F1	chr2:74347432-74347863	MCF-7	breast:	n/a	chr2:74347735-74347745
43	POLR2A	chr2:74347301-74347848	H1-neurons	neurons:	n/a	n/a
44	CTCFL	chr2:74347240-74347756	K562	blood:	n/a	chr2:74347428-74347437
45	ELF1	chr2:74347059-74347883	GM12878	blood:	n/a	n/a
46	SRF	chr2:74347158-74347863	MCF-7	breast:	n/a	n/a
47	MAX	chr2:74347353-74348004	H1-hESC	embryonic stem cell:	n/a	chr2:74347424-74347434
48	CTCF	chr2:74347316-74347579	MCF-7	breast:	n/a	n/a
49	NFIC	chr2:74347329-74347898	ECC-1	luminal epithelium:	n/a	n/a
50	YY1	chr2:74347047-74347876	GM12892	blood:	n/a	chr2:74347678-74347700 chr2:74347681-74347689 chr2:74347490-74347498 chr2:74347549-74347560 chr2:74347737-74347746 chr2:74347676-74347695 chr2:74347333-74347347 chr2:74347424-74347435 chr2:74347679-74347687 chr2:74347678-74347688

No.	Distal block	Cell Line	Cell type
1	chr2:74345450..74348977-chr2:74371413..74376785,7	MCF-7	breast:
2	chr16:2204962..2205609-chr2:74347432..74348083,2	Hela-S3	cervix:
3	chr2:74346224..74348120-chr2:74425405..74427108,2	MCF-7	breast:
4	chr2:74347177..74347948-chr2:74374539..74375360,2	MCF-7	breast:
5	chr1:89149816..89150316-chr2:74347319..74347820,2	Hela-S3	cervix:
6	chr2:74077294..74080205-chr2:74346163..74349130,2	K562	blood:
7	chr2:74347130..74350614-chr2:74373490..74375151,4	K562	blood:
8	chr2:74209017..74213063-chr2:74345530..74349441,7	MCF-7	breast:
9	chr2:74346117..74347922-chr2:74374665..74375603,8	MCF-7	breast:
10	chr2:74153590..74155495-chr2:74346048..74348829,2	MCF-7	breast:
11	chr2:74054992..74057413-chr2:74347412..74349314,2	K562	blood:
12	chr2:74346321..74348591-chr2:74373615..74376560,4	MCF-7	breast:
13	chr2:74345336..74350949-chr2:74424473..74426826,5	K562	blood:
14	chr17:7382544..7383272-chr2:74347263..74347881,2	Hela-S3	cervix:
15	chr2:74211217..74213609-chr2:74345958..74348496,2	MCF-7	breast:
16	chr2:74346058..74349268-chr2:74424477..74426947,5	K562	blood:
17	chr11:71823591..71824486-chr2:74346899..74347812,2	Hela-S3	cervix:
18	chr2:74209066..74214459-chr2:74345671..74349502,5	K562	blood:
19	chr2:74347151..74347932-chr6:159290392..159290973,2	Hela-S3	cervix:
20	chr2:74347109..74347870-chr2:74374605..74375136,2	K562	blood:
21	chr2:74347518..74349564-chr2:74361288..74362886,2	MCF-7	breast:
22	chr2:74345940..74348146-chr2:74432915..74434982,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC073263.1-3	chr2:74345408-74349576	NONHSAT071660

Variant related genes	Relation type
FNBP1P1	TF binding region
ENSG00000260260	Chromatin interaction
ENSG00000206630	Chromatin interaction
ENSG00000124356	Chromatin interaction
ENSG00000235499	Chromatin interaction
ENSG00000255989	Chromatin interaction
ENSG00000203711	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000217702	Chromatin interaction
ENSG00000225439	Chromatin interaction
ENSG00000110200	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000114956	Chromatin interaction
ENSG00000163170	Chromatin interaction
ENSG00000065243	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1667613	0.90[EUR][1000 genomes]
rs1667614	0.89[EUR][1000 genomes]
rs1667618	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1723289	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099824	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4271791	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715731	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs828844	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs828866	0.93[ASN][1000 genomes]
rs828899	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs828900	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874284	chr2:74283728-74348797	Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv874285	chr2:74283728-74355244	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1667619	FNBP1P1	cis	Skin Sun Exposed Lower leg	GTEx
rs1667619	FNBP1P1	cis	Muscle Skeletal	GTEx
rs1667619	FNBP1P1	cis	Adipose Subcutaneous	GTEx
rs1667619	FNBP1P1	cis	Artery Tibial	GTEx
rs1667619	FNBP1P1	cis	Esophagus Mucosa	GTEx
rs1667619	FNBP1P1	cis	Heart Left Ventricle	GTEx
rs1667619	FNBP1P1	cis	Nerve Tibial	GTEx
rs1667619	FNBP1P1	cis	lung	GTEx
rs1667619	FNBP1P1	cis	Thyroid	GTEx
rs1667619	FNBP1P1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74346600-74347800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:74346600-74347800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr2:74346600-74347800	Active TSS	Fetal Lung	lung
4	chr2:74346600-74347800	Active TSS	Sigmoid Colon	Sigmoid Colon
5	chr2:74346600-74347800	Active TSS	K562	blood
6	chr2:74346600-74348000	Active TSS	Brain Anterior Caudate	brain
7	chr2:74346600-74348200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:74346800-74347600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:74346800-74347800	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr2:74346800-74347800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:74346800-74348000	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr2:74346800-74348000	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr2:74346800-74348000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr2:74346800-74348200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:74346800-74348200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:74346800-74348400	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr2:74346800-74348400	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr2:74347000-74347600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:74347000-74347600	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr2:74347000-74347600	Active TSS	Liver	Liver
21	chr2:74347000-74347600	Active TSS	Brain Germinal Matrix	brain
22	chr2:74347000-74347600	Active TSS	GM12878-XiMat	blood
23	chr2:74347000-74347800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr2:74347000-74347800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:74347000-74347800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:74347000-74347800	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr2:74347000-74347800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:74347000-74347800	Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr2:74347000-74347800	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr2:74347000-74347800	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr2:74347000-74347800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:74347000-74347800	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr2:74347000-74347800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr2:74347000-74347800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr2:74347000-74347800	Active TSS	Esophagus	oesophagus
36	chr2:74347000-74347800	Active TSS	Rectal Smooth Muscle	rectum
37	chr2:74347000-74347800	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr2:74347000-74347800	Active TSS	HSMMtube	muscle
39	chr2:74347000-74347800	Active TSS	Monocytes-CD14+_RO01746	blood
40	chr2:74347000-74347800	Active TSS	NHEK	skin
41	chr2:74347000-74348000	Active TSS	H1 Cell Line	embryonic stem cell
42	chr2:74347000-74348000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:74347000-74348000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr2:74347000-74348000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:74347000-74348000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:74347000-74348000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:74347000-74348000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:74347000-74348000	Active TSS	Brain Angular Gyrus	brain
49	chr2:74347000-74348000	Active TSS	Brain Hippocampus Middle	brain
50	chr2:74347000-74348000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links