Variant report

Variant	rs1856303
Chromosome Location	chr1:169281238-169281239
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	EP300	chr1:169281194-169282005	SK-N-SH	brain:	n/a	n/a
2	USF1	chr1:169281186-169281921	K562	blood:	n/a	n/a
3	CEBPD	chr1:169281168-169281990	K562	blood:	n/a	n/a
4	JUND	chr1:169281215-169281999	SK-N-SH	brain:	n/a	n/a
5	TEAD4	chr1:169281115-169282052	K562	blood:	n/a	n/a
6	HMGN3	chr1:169281232-169281968	K562	blood:	n/a	n/a
7	JUND	chr1:169281225-169281980	SK-N-SH	brain:	n/a	n/a
8	ARID3A	chr1:169281179-169282005	K562	blood:	n/a	n/a
9	GATA1	chr1:169281007-169281975	PBDE	blood:	n/a	chr1:169281457-169281467
10	BHLHE40	chr1:169281212-169281825	K562	blood:	n/a	n/a
11	TCF12	chr1:169281143-169281973	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr1:169281185-169281973	PBDE	blood:	n/a	n/a
13	MAFK	chr1:169281068-169281875	K562	blood:	n/a	n/a
14	PBX3	chr1:169281217-169281870	SK-N-SH	brain:	n/a	n/a
15	CBX3	chr1:169281110-169281886	K562	blood:	n/a	n/a
16	FOSL2	chr1:169281217-169281934	SK-N-SH	brain:	n/a	n/a
17	USF1	chr1:169281193-169281922	HCT-116	colon:	n/a	n/a
18	GATA3	chr1:169281229-169282087	SK-N-SH	brain:	n/a	chr1:169281457-169281467
19	SIN3AK20	chr1:169281189-169281997	MCF-7	breast:	n/a	n/a
20	NFIC	chr1:169281217-169281965	SK-N-SH	brain:	n/a	n/a
21	JUND	chr1:169281189-169282028	SK-N-SH	brain:	n/a	n/a
22	GATA3	chr1:169281121-169282130	SK-N-SH	brain:	n/a	chr1:169281457-169281467
23	TCF12	chr1:169281133-169282042	SK-N-SH	brain:	n/a	n/a
24	FOSL1	chr1:169281216-169281970	HCT-116	colon:	n/a	n/a
25	MAX	chr1:169281235-169281933	HCT-116	colon:	n/a	n/a
26	CBX3	chr1:169281152-169281893	HCT-116	colon:	n/a	n/a
27	IRF1	chr1:169281150-169282111	K562	blood:	n/a	chr1:169281730-169281744
28	GATA3	chr1:169281197-169282188	MCF-7	breast:	n/a	chr1:169281457-169281467
29	E2F4	chr1:169281140-169281726	MCF10A-Er-Src	breast:	n/a	n/a
30	JUN	chr1:169280654-169282281	K562	blood:	n/a	chr1:169280809-169280817
31	REST	chr1:169281218-169281836	PFSK-1	brain:	n/a	n/a
32	CEBPD	chr1:169281066-169281922	K562	blood:	n/a	n/a
33	TRIM28	chr1:169281208-169281933	K562	blood:	n/a	n/a
34	PML	chr1:169281208-169281891	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169280326..169283147-chr1:169287038..169289000,3	K562	blood:
2	chr1:169281102..169283906-chr1:169293701..169295205,2	K562	blood:

Variant related genes	Relation type
NME7	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1018831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10429893	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10732287	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10753785	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10753786	0.96[CEU][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs10800408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10800414	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10800424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800435	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes]
rs10800438	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10800440	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10919105	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10919124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10919132	0.96[CEU][hapmap];0.86[TSI][hapmap];0.89[YRI][hapmap];0.89[EUR][1000 genomes]
rs10919174	0.82[JPT][hapmap]
rs1200076	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1200077	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1200079	0.82[JPT][hapmap]
rs1200083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1200085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1200161	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1200164	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1208135	0.82[JPT][hapmap]
rs1208327	0.81[ASN][1000 genomes]
rs1208370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1208371	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1208375	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1208377	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12086665	0.82[JPT][hapmap]
rs12752748	0.82[JPT][hapmap]
rs1400836	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1400839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517744	0.82[JPT][hapmap]
rs1517747	0.82[JPT][hapmap]
rs1591733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861990	0.82[JPT][hapmap]
rs17345107	0.82[JPT][hapmap]
rs17349222	0.82[JPT][hapmap]
rs1829286	0.81[ASN][1000 genomes]
rs1829287	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1850525	0.82[EUR][1000 genomes]
rs1983546	0.82[JPT][hapmap]
rs2037250	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066000	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138898	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2152979	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176473	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2176474	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2211017	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300158	0.96[CEU][hapmap];0.89[YRI][hapmap];0.89[EUR][1000 genomes]
rs2420008	0.82[JPT][hapmap]
rs3766057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3766095	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs3905328	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs4264046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300284	0.81[AMR][1000 genomes]
rs4454599	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4656183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs4656672	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6427185	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs6656822	0.82[JPT][hapmap]
rs6662237	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691226	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7415756	0.89[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs7533257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552323	0.82[JPT][hapmap]
rs994986	1.00[CHB][hapmap];0.82[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1856303	NME7	cis	Artery Aorta	GTEx
rs1856303	NME7	cis	Artery Tibial	GTEx
rs1856303	NME7	cis	multi-tissue	Pritchard
rs1856303	NME7	cis	Nerve Tibial	GTEx
rs1856303	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs1856303	NME7	cis	Thyroid	GTEx
rs1856303	NME7	cis	Stomach	GTEx
rs1856303	NME7	cis	lung	GTEx
rs1856303	NME7	cis	Esophagus Muscularis	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169257600-169284800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr1:169259600-169294400	Weak transcription	Pancreas	Pancrea
3	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
4	chr1:169264000-169281400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:169264400-169294400	Weak transcription	Left Ventricle	heart
6	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
7	chr1:169269200-169281400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:169269400-169281600	Weak transcription	HUVEC	blood vessel
9	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:169271800-169297200	Weak transcription	Psoas Muscle	Psoas
11	chr1:169273600-169312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:169275200-169281400	Weak transcription	Fetal Thymus	thymus
13	chr1:169276400-169281400	Weak transcription	HSMMtube	muscle
14	chr1:169276800-169304600	Weak transcription	Ovary	ovary
15	chr1:169277000-169294600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:169277000-169306200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:169278000-169285800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:169279000-169281400	Weak transcription	Primary B cells from cord blood	blood
19	chr1:169279000-169281400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:169279000-169281400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:169279000-169282000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:169279000-169288400	Weak transcription	Brain Angular Gyrus	brain
23	chr1:169279000-169291200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:169279000-169293800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:169279000-169295600	Weak transcription	Adipose Nuclei	Adipose
26	chr1:169279200-169281400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:169279200-169281400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:169279200-169282000	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr1:169279200-169287200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:169279200-169296000	Weak transcription	Primary T cells from cord blood	blood
31	chr1:169279400-169281600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr1:169279800-169281400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr1:169280200-169304600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:169280800-169282200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:169281000-169282000	Enhancers	Fetal Intestine Large	intestine
36	chr1:169281000-169282000	Enhancers	A549	lung
37	chr1:169281000-169282000	Enhancers	Dnd41	blood
38	chr1:169281000-169282000	Flanking Active TSS	K562	blood
39	chr1:169281000-169282000	Enhancers	NHLF	lung
40	chr1:169281000-169282200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:169281000-169282800	Enhancers	Hela-S3	cervix
42	chr1:169281200-169281400	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr1:169281200-169281400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:169281200-169281400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr1:169281200-169281600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:169281200-169281600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:169281200-169281600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:169281200-169281600	Enhancers	Fetal Intestine Small	intestine
49	chr1:169281200-169281800	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr1:169281200-169282000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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