Variant report

Variant	rs1517749
Chromosome Location	chr1:169296496-169296497
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	FOSL2	chr1:169296015-169296629	SK-N-SH	brain:	n/a	n/a
2	FOS	chr1:169296152-169296501	MCF10A-Er-Src	breast:	n/a	chr1:169296330-169296341
3	JUND	chr1:169296059-169296632	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr1:169296027-169296675	SK-N-SH	brain:	n/a	n/a
5	JUND	chr1:169296134-169296536	K562	blood:	n/a	n/a
6	STAT3	chr1:169296161-169296505	MCF10A-Er-Src	breast:	n/a	chr1:169296342-169296349
7	IRF1	chr1:169296172-169296505	K562	blood:	n/a	chr1:169296176-169296189
8	JUND	chr1:169296010-169296538	HCT-116	colon:	n/a	n/a
9	TBL1XR1	chr1:169296095-169296500	K562	blood:	n/a	n/a
10	CUX1	chr1:169296044-169296590	K562	blood:	n/a	n/a
11	FOSL1	chr1:169296106-169296614	HCT-116	colon:	n/a	chr1:169296330-169296341
12	GATA2	chr1:169296160-169296530	HUVEC	blood vessel:	n/a	n/a
13	FOS	chr1:169296150-169296503	MCF10A-Er-Src	breast:	n/a	chr1:169296330-169296341
14	FOS	chr1:169296002-169296591	HUVEC	blood vessel:	n/a	chr1:169296330-169296341
15	GATA2	chr1:169296172-169296538	K562	blood:	n/a	n/a
16	TEAD4	chr1:169295927-169296548	K562	blood:	n/a	n/a
17	TAL1	chr1:169296207-169296532	K562	blood:	n/a	n/a
18	JUN	chr1:169296178-169296514	HUVEC	blood vessel:	n/a	n/a
19	CBX3	chr1:169296071-169296561	K562	blood:	n/a	n/a
20	FOSL1	chr1:169296204-169296505	K562	blood:	n/a	chr1:169296330-169296341
21	EP300	chr1:169296019-169296552	K562	blood:	n/a	n/a
22	GATA1	chr1:169295736-169296662	PBDE	blood:	n/a	n/a
23	FOS	chr1:169296122-169296527	MCF10A-Er-Src	breast:	n/a	chr1:169296330-169296341
24	FOSL2	chr1:169296059-169296530	A549	lung:	n/a	n/a
25	FOS	chr1:169296149-169296767	MCF10A-Er-Src	breast:	n/a	chr1:169296330-169296341
26	NFIC	chr1:169296027-169296572	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169279086..169281627-chr1:169295579..169298053,2	K562	blood:
2	chr1:169291437..169294345-chr1:169295475..169297579,2	K562	blood:

Variant related genes	Relation type
NME7	TF binding region
ENSG00000143156	Chromatin interaction
ENSG00000235575	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1011638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494477	1.00[ASN][1000 genomes]
rs10737545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800423	0.86[EUR][1000 genomes]
rs10800429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800431	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800433	1.00[ASN][1000 genomes]
rs10800434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919125	1.00[ASN][1000 genomes]
rs10919127	1.00[ASN][1000 genomes]
rs10919128	1.00[ASN][1000 genomes]
rs10919130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919133	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919134	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919144	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919147	1.00[ASN][1000 genomes]
rs12029800	1.00[ASN][1000 genomes]
rs12030541	1.00[ASN][1000 genomes]
rs12030810	1.00[ASN][1000 genomes]
rs12031371	1.00[ASN][1000 genomes]
rs12031830	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12036426	1.00[ASN][1000 genomes]
rs12042082	1.00[ASN][1000 genomes]
rs12042990	1.00[ASN][1000 genomes]
rs12045803	1.00[ASN][1000 genomes]
rs12567342	1.00[ASN][1000 genomes]
rs1517750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17345426	1.00[ASN][1000 genomes]
rs1856302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2090514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4497270	0.81[ASN][1000 genomes]
rs4534447	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4562680	0.86[ASN][1000 genomes]
rs61806987	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7413522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528142	1.00[ASN][1000 genomes]
rs7556463	1.00[ASN][1000 genomes]
rs929132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929133	0.89[EUR][1000 genomes]
rs9887925	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv429913	chr1:169177019-169296744	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1012919	chr1:169200982-169324750	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1517749	NME7	cis	Esophagus Mucosa	GTEx
rs1517749	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs1517749	NME7	cis	Thyroid	GTEx
rs1517749	NME7	cis	Nerve Tibial	GTEx
rs1517749	NME7	cis	Artery Tibial	GTEx
rs1517749	NME7	cis	Esophagus Muscularis	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
2	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
3	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:169271800-169297200	Weak transcription	Psoas Muscle	Psoas
5	chr1:169273600-169312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:169276800-169304600	Weak transcription	Ovary	ovary
7	chr1:169277000-169306200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:169280200-169304600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:169281600-169306600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:169282000-169306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:169288600-169297200	Weak transcription	Small Intestine	intestine
12	chr1:169291000-169313200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:169294000-169305200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:169294600-169297600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr1:169294600-169307400	Weak transcription	Gastric	stomach
16	chr1:169294800-169297200	Weak transcription	Left Ventricle	heart
17	chr1:169294800-169299600	Weak transcription	Fetal Intestine Small	intestine
18	chr1:169295400-169296600	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr1:169295400-169296600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:169295400-169297400	Enhancers	Primary hematopoietic stem cells	blood
21	chr1:169295600-169296600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:169295600-169296600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:169295600-169296600	Flanking Active TSS	A549	lung
24	chr1:169295600-169296600	Enhancers	HMEC	breast
25	chr1:169295600-169296600	Flanking Active TSS	HUVEC	blood vessel
26	chr1:169295600-169296600	Enhancers	NH-A	brain
27	chr1:169295800-169296600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:169295800-169296600	Enhancers	GM12878-XiMat	blood
29	chr1:169295800-169296800	Enhancers	NHEK	skin
30	chr1:169295800-169297200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:169296000-169296600	Enhancers	Muscle Satellite Cultured Cells	--
32	chr1:169296000-169296600	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr1:169296000-169296600	Enhancers	Osteobl	bone
34	chr1:169296000-169297200	Enhancers	K562	blood
35	chr1:169296200-169296600	Enhancers	NHDF-Ad	bronchial
36	chr1:169296200-169297800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:169296400-169306600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links