Variant report

Variant	rs471688
Chromosome Location	chr12:121285424-121285425
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	FOS	chr12:121285252-121285501	MCF10A-Er-Src	breast:	n/a	n/a
2	RUNX3	chr12:121285326-121286277	GM12878	blood:	n/a	n/a
3	JUND	chr12:121285251-121285695	HCT-116	colon:	n/a	n/a
4	ELF1	chr12:121285318-121285687	GM12878	blood:	n/a	n/a
5	FOS	chr12:121285260-121285441	MCF10A-Er-Src	breast:	n/a	n/a
6	RUNX3	chr12:121285252-121286178	GM12878	blood:	n/a	n/a
7	FOS	chr12:121285237-121285437	MCF10A-Er-Src	breast:	n/a	n/a
8	MTA3	chr12:121285254-121286046	GM12878	blood:	n/a	n/a
9	FOS	chr12:121285237-121285484	MCF10A-Er-Src	breast:	n/a	n/a
10	ZNF384	chr12:121285244-121285516	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:121284720..121286332-chr12:121290544..121292082,2	K562	blood:
2	chr12:120727503..120731222-chr12:121282952..121285914,3	MCF-7	breast:
3	chr12:121259584..121261305-chr12:121284288..121286336,2	K562	blood:

Variant related genes	Relation type
ARF1P2	TF binding region
ENSG00000202538	Chromatin interaction
ENSG00000200795	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1027556	0.87[YRI][hapmap]
rs1039302	0.86[YRI][hapmap]
rs10431387	0.86[YRI][hapmap]
rs10437838	0.86[YRI][hapmap]
rs10774568	0.84[YRI][hapmap]
rs10774569	0.87[YRI][hapmap]
rs10774571	0.87[YRI][hapmap]
rs10774572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10849786	0.82[YRI][hapmap]
rs10849788	0.82[YRI][hapmap]
rs10849791	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10849807	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10849810	0.87[YRI][hapmap]
rs10849811	0.87[YRI][hapmap]
rs11065259	0.87[YRI][hapmap]
rs11065264	0.81[ASN][1000 genomes]
rs11065282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065283	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065284	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065293	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065298	0.87[YRI][hapmap]
rs11065300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11065307	0.83[ASN][1000 genomes]
rs11065311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11065322	0.86[YRI][hapmap]
rs11065324	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1151849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151859	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11608262	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11611087	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168944	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168946	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168948	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168953	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1177585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1179939	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12371178	0.83[ASN][1000 genomes]
rs12580949	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs12809299	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12822123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12825746	0.98[ASN][1000 genomes]
rs12831094	0.84[ASN][1000 genomes]
rs13746	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1542859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1696357	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1718180	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2015462	0.81[ASN][1000 genomes]
rs2047568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2393717	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2393718	0.85[YRI][hapmap]
rs2461475	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650017	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2893876	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3213566	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3213567	0.81[ASN][1000 genomes]
rs3213568	0.86[YRI][hapmap]
rs3213570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3213571	0.87[YRI][hapmap]
rs3213572	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34009825	0.83[ASN][1000 genomes]
rs34076777	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35706672	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35905305	0.82[ASN][1000 genomes]
rs3809313	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3809314	0.86[YRI][hapmap]
rs3842985	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3861797	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3883901	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3897746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3901854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4454799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4766979	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4766980	0.84[ASN][1000 genomes]
rs4767937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs487943	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs508595	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs520753	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs531782	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533264	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs548452	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs572016	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577961	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580240	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58291418	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58918988	0.82[ASN][1000 genomes]
rs590625	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602984	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs608394	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs609700	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs610694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs618482	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs624216	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625228	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs647881	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6489780	0.86[YRI][hapmap]
rs6489782	0.82[YRI][hapmap]
rs661647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665585	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs666976	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs668622	0.80[ASN][1000 genomes]
rs7135147	0.86[YRI][hapmap]
rs7137504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7139145	0.87[YRI][hapmap]
rs715319	0.86[YRI][hapmap]
rs7298639	0.87[YRI][hapmap]
rs73413868	0.84[ASN][1000 genomes]
rs7965332	0.87[YRI][hapmap]
rs7969140	0.84[ASN][1000 genomes]
rs869781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs909053	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs989986	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs989987	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs471688	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs471688	RPLP0	cis	Skin Sun Exposed Lower leg	GTEx
rs471688	UNQ1887	cis	Temporal Cortex	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121267600-121285800	Weak transcription	Colonic Mucosa	Colon
2	chr12:121269800-121291400	Weak transcription	Fetal Intestine Large	intestine
3	chr12:121272800-121285600	Weak transcription	Hela-S3	cervix
4	chr12:121274000-121285800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:121274000-121287200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:121274200-121291800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:121274400-121285800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:121274400-121289400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr12:121274600-121289000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:121274600-121289800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr12:121274800-121291800	Weak transcription	Dnd41	blood
12	chr12:121277600-121287200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:121279200-121289200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:121279400-121286400	Enhancers	Brain Substantia Nigra	brain
15	chr12:121279600-121286600	Enhancers	Brain Hippocampus Middle	brain
16	chr12:121280800-121287400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:121281600-121296200	Weak transcription	HepG2	liver
18	chr12:121281800-121286000	Enhancers	Colon Smooth Muscle	Colon
19	chr12:121282000-121286400	Enhancers	Right Ventricle	heart
20	chr12:121282000-121308600	Weak transcription	Fetal Kidney	kidney
21	chr12:121282400-121285600	Weak transcription	K562	blood
22	chr12:121282400-121285800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:121282400-121286200	Weak transcription	HMEC	breast
24	chr12:121282600-121285600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr12:121282600-121285600	Weak transcription	Fetal Heart	heart
26	chr12:121282600-121288400	Enhancers	Psoas Muscle	Psoas
27	chr12:121283000-121285800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:121283000-121287600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:121283000-121287600	Weak transcription	NHLF	lung
30	chr12:121283200-121285600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:121283200-121285800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:121283200-121287600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:121283200-121288600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr12:121283200-121289200	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr12:121283200-121291200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:121283200-121310200	Weak transcription	Placenta	Placenta
37	chr12:121283400-121285600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr12:121283400-121285800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr12:121283400-121289400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr12:121283400-121289400	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:121283400-121291800	Weak transcription	Pancreas	Pancrea
42	chr12:121283400-121307400	Weak transcription	Esophagus	oesophagus
43	chr12:121283600-121285600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:121283600-121285600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr12:121283600-121285600	Enhancers	GM12878-XiMat	blood
46	chr12:121283600-121287400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:121283600-121290800	Weak transcription	Gastric	stomach
48	chr12:121283600-121295600	Weak transcription	Fetal Stomach	stomach
49	chr12:121283600-121302200	Weak transcription	Lung	lung
50	chr12:121283800-121285800	Weak transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links