Variant report

Variant	rs1641879
Chromosome Location	chr16:12638333-12638334
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	POLR2A	chr16:12636690-12639643	GM12878	blood:	n/a	n/a
2	POLR2A	chr16:12636727-12640562	GM12891	blood:	n/a	n/a
3	SPI1	chr16:12637932-12638346	GM12878	blood:	n/a	n/a
4	TBP	chr16:12637900-12638352	GM12878	blood:	n/a	n/a
5	YY1	chr16:12638020-12638375	GM12878	blood:	n/a	n/a
6	NFATC1	chr16:12637816-12638403	GM12878	blood:	n/a	n/a
7	TCF12	chr16:12637978-12638388	GM12878	blood:	n/a	n/a
8	IKZF1	chr16:12637278-12638463	GM12878	blood:	n/a	n/a
9	PML	chr16:12637891-12638634	GM12878	blood:	n/a	n/a
10	CEBPB	chr16:12636781-12638818	GM12878	blood:	n/a	n/a
11	POLR2A	chr16:12637775-12638476	GM12892	blood:	n/a	n/a
12	PAX5	chr16:12637803-12638395	GM12878	blood:	n/a	chr16:12638060-12638069 chr16:12638291-12638300
13	EBF1	chr16:12637940-12638340	GM12878	blood:	n/a	n/a
14	FOSL2	chr16:12637573-12638743	HepG2	liver:	n/a	chr16:12638441-12638453
15	RUNX3	chr16:12637025-12638988	GM12878	blood:	n/a	n/a
16	SPI1	chr16:12637928-12638340	GM12891	blood:	n/a	n/a
17	BCLAF1	chr16:12637158-12638446	GM12878	blood:	n/a	n/a
18	MTA3	chr16:12636658-12638831	GM12878	blood:	n/a	n/a
19	POLR2A	chr16:12636855-12640530	GM12891	blood:	n/a	n/a
20	SPI1	chr16:12637889-12638391	GM12891	blood:	n/a	n/a
21	NFIC	chr16:12637028-12638572	GM12878	blood:	n/a	n/a
22	FOXM1	chr16:12637020-12638438	GM12878	blood:	n/a	n/a
23	ARID3A	chr16:12637659-12638979	HepG2	liver:	n/a	n/a
24	POLR2A	chr16:12638137-12638334	GM12878	blood:	n/a	n/a
25	POLR2A	chr16:12637143-12640374	GM12878	blood:	n/a	n/a
26	MTA3	chr16:12636806-12639043	GM12878	blood:	n/a	n/a
27	BCL11A	chr16:12637890-12638396	GM12878	blood:	n/a	n/a
28	POLR2A	chr16:12636967-12640529	GM12878	blood:	n/a	n/a
29	CUX1	chr16:12637882-12638337	GM12878	blood:	n/a	n/a
30	TEAD4	chr16:12637404-12638976	HepG2	liver:	n/a	n/a
31	POLR2A	chr16:12637840-12638439	GM12892	blood:	n/a	n/a
32	POLR2A	chr16:12637742-12638529	HepG2	liver:	n/a	n/a
33	RUNX3	chr16:12637080-12638420	GM12878	blood:	n/a	n/a
34	SPI1	chr16:12638006-12638362	HL-60	blood:	n/a	n/a
35	NFIC	chr16:12637805-12638540	GM12878	blood:	n/a	n/a
36	BCLAF1	chr16:12637669-12638335	GM12878	blood:	n/a	n/a
37	SPI1	chr16:12637691-12638651	GM12878	blood:	n/a	n/a
38	STAT5A	chr16:12637827-12638649	GM12878	blood:	n/a	chr16:12638184-12638192
39	STAT5A	chr16:12637989-12638541	GM12878	blood:	n/a	chr16:12638184-12638192
40	ATF2	chr16:12637898-12638419	GM12878	blood:	n/a	n/a
41	IRF4	chr16:12637839-12638388	GM12878	blood:	n/a	n/a
42	EBF1	chr16:12637822-12638355	GM12878	blood:	n/a	n/a
43	ATF2	chr16:12637025-12638683	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000260601	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1007324	0.88[EUR][1000 genomes]
rs10492794	0.94[EUR][1000 genomes]
rs10852350	0.85[EUR][1000 genomes]
rs11075089	0.85[EUR][1000 genomes]
rs11075090	0.84[EUR][1000 genomes]
rs11640491	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11642326	0.85[EUR][1000 genomes]
rs11643978	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11645403	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11645654	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11645856	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11645899	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11647147	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1540279	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1614433	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1615250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618096	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1641873	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1641877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1641881	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1641889	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1641890	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1641893	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17240735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819472	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1794306	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794307	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794313	0.94[EUR][1000 genomes]
rs1794315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1794316	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1970769	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006159	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2213293	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301217	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301218	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2301219	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2856784	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2865230	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2902959	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2902961	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764301	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3975365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4390575	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4513084	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62026884	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62026887	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62026956	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62026957	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187812	0.84[EUR][1000 genomes]
rs728583	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728584	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9788839	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1051242	chr16:12482972-12897243	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv542749	chr16:12482972-12897243	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1035581	chr16:12516946-12863700	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1051607	chr16:12522130-13347676	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv542750	chr16:12522130-13347676	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv571465	chr16:12625395-12639800	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1054084	chr16:12625727-12650247	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv431433	chr16:12628409-12654408	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv1842867	chr16:12632286-12678721	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1039338	chr16:12632918-12642955	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1040887	chr16:12632918-12650247	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv2751546	chr16:12635498-12674704	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv1040358	chr16:12636982-12650247	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1641879	C16orf68	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12613000-12670800	Weak transcription	Pancreas	Pancrea
2	chr16:12625800-12643400	Weak transcription	Gastric	stomach
3	chr16:12627000-12642200	Weak transcription	Right Ventricle	heart
4	chr16:12630400-12638800	Weak transcription	Fetal Thymus	thymus
5	chr16:12632800-12638600	Weak transcription	Lung	lung
6	chr16:12632800-12640200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr16:12632800-12641000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr16:12632800-12646600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr16:12632800-12663800	Weak transcription	Aorta	Aorta
10	chr16:12633000-12638400	Weak transcription	Brain Angular Gyrus	brain
11	chr16:12633000-12638400	Weak transcription	Brain Hippocampus Middle	brain
12	chr16:12633000-12646600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr16:12633200-12638400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr16:12633200-12640600	Weak transcription	Stomach Mucosa	stomach
15	chr16:12633200-12640800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr16:12633400-12654400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr16:12633600-12638400	Weak transcription	Brain Substantia Nigra	brain
18	chr16:12633600-12639000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr16:12633600-12640000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr16:12633800-12640000	Weak transcription	NHEK	skin
21	chr16:12634200-12638600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr16:12634200-12640600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr16:12635000-12644200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr16:12635200-12638600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr16:12635400-12639000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr16:12635400-12640600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr16:12635600-12639200	Weak transcription	Esophagus	oesophagus
28	chr16:12635600-12641000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr16:12636000-12642600	Flanking Active TSS	GM12878-XiMat	blood
30	chr16:12636400-12640600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr16:12637000-12638600	Genic enhancers	Primary B cells from peripheral blood	blood
32	chr16:12637000-12638600	Strong transcription	Primary T cells from cord blood	blood
33	chr16:12637000-12638600	Enhancers	Fetal Muscle Leg	muscle
34	chr16:12637000-12638800	Enhancers	Fetal Muscle Trunk	muscle
35	chr16:12637200-12638400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr16:12637200-12639200	Flanking Active TSS	HepG2	liver
37	chr16:12637200-12642200	Enhancers	Spleen	Spleen
38	chr16:12637600-12641800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr16:12637600-12642400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr16:12637600-12642800	Enhancers	Primary B cells from cord blood	blood
41	chr16:12637800-12638800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr16:12638000-12638600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr16:12638000-12638800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr16:12638000-12638800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr16:12638000-12639400	Enhancers	HSMMtube	muscle
46	chr16:12638200-12639200	Enhancers	HSMM	muscle
47	chr16:12638200-12639200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr16:12638200-12641000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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