Variant report

Variant	rs10500384
Chromosome Location	chr16:12707379-12707380
allele	A/G
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	FOXA1	chr16:12706252-12708264	HepG2	liver:	n/a	n/a
2	RCOR1	chr16:12706536-12707757	K562	blood:	n/a	n/a
3	GATA2	chr16:12707370-12707841	K562	blood:	n/a	n/a
4	CEBPB	chr16:12707347-12708054	HCT-116	colon:	n/a	n/a
5	EP300	chr16:12706229-12708381	HepG2	liver:	n/a	n/a
6	GATA3	chr16:12707236-12708046	SK-N-SH	brain:	n/a	n/a
7	HNF4A	chr16:12707096-12707814	HepG2	liver:	n/a	chr16:12707395-12707409 chr16:12707395-12707409 chr16:12707396-12707409 chr16:12707395-12707408 chr16:12707395-12707409 chr16:12707396-12707408 chr16:12707394-12707409 chr16:12707393-12707411 chr16:12707396-12707408
8	GATA3	chr16:12707078-12707949	MCF-7	breast:	n/a	n/a
9	JUN	chr16:12706488-12708204	HepG2	liver:	n/a	n/a
10	RCOR1	chr16:12706929-12707434	GM12878	blood:	n/a	n/a
11	HNF4A	chr16:12707034-12707896	HepG2	liver:	n/a	chr16:12707395-12707409 chr16:12707395-12707409 chr16:12707396-12707409 chr16:12707395-12707408 chr16:12707395-12707409 chr16:12707396-12707408 chr16:12707394-12707409 chr16:12707393-12707411 chr16:12707396-12707408
12	PAX5	chr16:12707204-12707924	GM12878	blood:	n/a	n/a
13	EP300	chr16:12706434-12708296	HepG2	liver:	n/a	n/a
14	REST	chr16:12707020-12708185	A549	lung:	n/a	n/a
15	PML	chr16:12707235-12708035	GM12878	blood:	n/a	n/a
16	FOXM1	chr16:12707151-12707979	GM12878	blood:	n/a	n/a
17	MAX	chr16:12706139-12708451	A549	lung:	n/a	n/a
18	MAX	chr16:12707108-12708209	HepG2	liver:	n/a	n/a
19	FOXA2	chr16:12707055-12707536	A549	lung:	n/a	n/a
20	EP300	chr16:12707039-12707944	GM12878	blood:	n/a	n/a
21	TCF7L2	chr16:12707216-12707892	HCT-116	colon:	n/a	chr16:12707399-12707409 chr16:12707399-12707406 chr16:12707398-12707407 chr16:12707395-12707411 chr16:12707399-12707408 chr16:12707395-12707411
22	JUND	chr16:12707211-12708380	HCT-116	colon:	n/a	chr16:12707672-12707683 chr16:12707700-12707711
23	ATF3	chr16:12707254-12707910	A549	lung:	n/a	n/a
24	GATA3	chr16:12707255-12708078	MCF-7	breast:	n/a	n/a
25	EP300	chr16:12706287-12708137	HepG2	liver:	n/a	n/a
26	HNF4A	chr16:12706874-12707896	HepG2	liver:	n/a	chr16:12707395-12707409 chr16:12707395-12707409 chr16:12707396-12707409 chr16:12707395-12707408 chr16:12707395-12707409 chr16:12707396-12707408 chr16:12707394-12707409 chr16:12707393-12707411 chr16:12707396-12707408
27	POLR2A	chr16:12707218-12707518	HepG2	liver:	n/a	n/a
28	SMC3	chr16:12706452-12708092	HepG2	liver:	n/a	n/a
29	CUX1	chr16:12707256-12707779	K562	blood:	n/a	n/a
30	HEY1	chr16:12706306-12708350	HepG2	liver:	n/a	n/a
31	JUND	chr16:12707241-12707952	HepG2	liver:	n/a	chr16:12707672-12707683 chr16:12707700-12707711
32	FOXA1	chr16:12706997-12707917	HepG2	liver:	n/a	n/a
33	JUND	chr16:12707369-12708153	SK-N-SH	brain:	n/a	chr16:12707672-12707683 chr16:12707700-12707711
34	SP1	chr16:12707182-12707855	GM12878	blood:	n/a	n/a
35	MYC	chr16:12707175-12708099	K562	blood:	n/a	n/a
36	SIN3AK20	chr16:12707182-12708036	MCF-7	breast:	n/a	n/a
37	NR2F2	chr16:12707172-12707961	K562	blood:	n/a	n/a
38	MAFK	chr16:12707142-12708189	HepG2	liver:	n/a	n/a
39	CCNT2	chr16:12707190-12707831	K562	blood:	n/a	n/a
40	EBF1	chr16:12707245-12707777	GM12878	blood:	n/a	n/a
41	SP1	chr16:12707178-12707862	GM12878	blood:	n/a	n/a
42	EGR1	chr16:12707364-12708041	HCT-116	colon:	n/a	n/a
43	ZEB1	chr16:12706298-12708202	HepG2	liver:	n/a	n/a
44	CBX3	chr16:12707283-12707852	K562	blood:	n/a	n/a
45	MTA3	chr16:12707249-12707994	GM12878	blood:	n/a	n/a
46	REST	chr16:12707093-12707945	HepG2	liver:	n/a	n/a
47	ATF2	chr16:12706985-12707963	GM12878	blood:	n/a	n/a
48	JUN	chr16:12707263-12707894	K562	blood:	n/a	n/a
49	USF1	chr16:12707195-12708026	HCT-116	colon:	n/a	chr16:12707657-12707668 chr16:12707685-12707696
50	SP1	chr16:12707114-12708209	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:12705362..12710268-chr16:12710311..12712475,5	K562	blood:
2	chr16:12705693..12708514-chr16:12893374..12897390,4	K562	blood:

Variant related genes	Relation type
ENSG00000259899	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10500388	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11640050	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]
rs11645561	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11646824	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11866714	0.84[CHB][hapmap];0.82[CHD][hapmap];0.80[MEX][hapmap]
rs16960309	0.85[EUR][1000 genomes]
rs2115105	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3829527	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60172355	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62027344	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6498341	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8062155	1.00[YRI][hapmap]
rs9746526	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:36 , 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	nsv437802	chr16:12667076-12708294	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv571469	chr16:12670401-12715480	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv1804537	chr16:12671491-12708186	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	esv18351	chr16:12674207-12734557	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv2757629	chr16:12676745-12712199	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv2758631	chr16:12676745-12712199	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv1812058	chr16:12680270-12712059	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv9351	chr16:12681377-12708042	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1051014	chr16:12683657-12722792	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	esv1812319	chr16:12685000-12707419	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	esv1813426	chr16:12685000-12707419	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
19	nsv1038888	chr16:12685122-12707419	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv1052847	chr16:12685133-12707379	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
21	nsv1036322	chr16:12690859-12707379	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv1048667	chr16:12690859-12707419	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	esv2760435	chr16:12690859-12707737	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
24	nsv1048793	chr16:12690859-12707737	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
25	nsv1037906	chr16:12690859-12708208	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
26	nsv1045233	chr16:12690859-12708294	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
27	nsv1041721	chr16:12690859-12708403	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
28	esv2753317	chr16:12691532-12707379	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
29	esv1811848	chr16:12691643-12708186	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
30	esv1808513	chr16:12691653-12711233	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
31	esv1813801	chr16:12691653-12711233	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
32	nsv905351	chr16:12697211-12721188	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
33	nsv471083	chr16:12704140-12714394	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
34	nsv457422	chr16:12705930-12711025	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
35	nsv571478	chr16:12705930-12711025	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
36	esv1819970	chr16:12705930-12712304	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10500384	LOC92017	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12703800-12708000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr16:12704000-12708800	Enhancers	Placenta	Placenta
3	chr16:12704200-12708400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr16:12704400-12707400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr16:12704400-12707400	Enhancers	Stomach Mucosa	stomach
6	chr16:12704600-12708200	Enhancers	NHEK	skin
7	chr16:12704800-12709400	Enhancers	Fetal Intestine Large	intestine
8	chr16:12705000-12707800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr16:12705000-12709000	Enhancers	Fetal Intestine Small	intestine
10	chr16:12706000-12708800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr16:12706200-12708000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr16:12706400-12707400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr16:12706400-12707400	Enhancers	Primary hematopoietic stem cells	blood
14	chr16:12706400-12708200	Enhancers	NH-A	brain
15	chr16:12706400-12708400	Flanking Active TSS	HepG2	liver
16	chr16:12706400-12708400	Enhancers	HMEC	breast
17	chr16:12706400-12709000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr16:12706400-12709000	Enhancers	Fetal Thymus	thymus
19	chr16:12706600-12707600	Enhancers	Dnd41	blood
20	chr16:12706600-12708200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr16:12706600-12708200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr16:12706600-12708600	Enhancers	H9 Cell Line	embryonic stem cell
23	chr16:12706600-12708600	Enhancers	Thymus	Thymus
24	chr16:12706600-12708600	Enhancers	GM12878-XiMat	blood
25	chr16:12706600-12708800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr16:12706800-12707600	Flanking Active TSS	K562	blood
27	chr16:12706800-12708800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr16:12707000-12708000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr16:12707000-12708400	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr16:12707200-12707400	Enhancers	HSMM	muscle
31	chr16:12707200-12707600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr16:12707200-12707600	Active TSS	A549	lung
33	chr16:12707200-12707800	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr16:12707200-12708000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr16:12707200-12708000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr16:12707200-12708200	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr16:12707200-12708400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr16:12707200-12708400	Enhancers	Liver	Liver
39	chr16:12707200-12708400	Bivalent Enhancer	Hela-S3	cervix
40	chr16:12707200-12709000	Enhancers	HUES64 Cell Line	embryonic stem cell

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