Variant report

Variant	rs1669884
Chromosome Location	chr12:42844398-42844399
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	PBX3	chr12:42843906-42844571	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr12:42843893-42844418	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr12:42843804-42844552	SK-N-SH	brain:	n/a	chr12:42843938-42843954
4	TCF12	chr12:42843930-42844632	SK-N-SH	brain:	n/a	n/a
5	EP300	chr12:42843965-42844439	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr12:42842683-42845517	K562	blood:	n/a	n/a
7	EP300	chr12:42844002-42844494	SK-N-SH_RA	brain:	n/a	n/a
8	PBX3	chr12:42843838-42844552	SK-N-SH	brain:	n/a	n/a
9	EP300	chr12:42843854-42844566	SK-N-SH	brain:	n/a	n/a
10	NFIC	chr12:42843948-42844478	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr12:42843068-42845640	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr12:42843697-42844629	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr12:42843330-42844952	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr12:42844173-42844410	HUVEC	blood vessel:	n/a	n/a
15	NFIC	chr12:42843867-42844469	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000207142	TF binding region

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1043652	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1043656	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10880279	0.92[CEU][hapmap]
rs10880282	0.82[EUR][1000 genomes]
rs10880284	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs11181421	0.85[EUR][1000 genomes]
rs11181427	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11181453	0.92[EUR][1000 genomes]
rs11181484	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12229224	0.89[EUR][1000 genomes]
rs12229266	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12230583	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12231335	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12422938	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12423383	1.00[CEU][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12425945	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12578312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1376931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1629725	0.93[EUR][1000 genomes]
rs1669888	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1669890	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1669891	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1669894	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1669895	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1669897	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1669898	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1669899	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1669900	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1669901	0.93[EUR][1000 genomes]
rs1669903	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1669905	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669911	0.92[EUR][1000 genomes]
rs1669912	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1669913	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1669914	0.93[EUR][1000 genomes]
rs1669935	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1669937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796354	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1796355	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1796356	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796357	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1796359	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796360	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1796365	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1796373	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796374	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1796377	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796379	0.92[EUR][1000 genomes]
rs1796385	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1796387	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1796389	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1796392	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1796395	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1796396	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1796397	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1796398	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1961953	0.88[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs2053946	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2243465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2406872	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2406969	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2600911	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2600912	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2600916	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2600917	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2600918	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708063	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708069	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2708075	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2708077	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2708506	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2952653	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213989	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3747562	0.81[CEU][hapmap]
rs3747563	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3761677	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3827524	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4603368	0.91[EUR][1000 genomes]
rs4768397	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs4768398	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4768401	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4768412	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7134895	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs721447	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73122408	0.92[EUR][1000 genomes]
rs73122414	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73122418	0.92[EUR][1000 genomes]
rs7486516	0.80[ASN][1000 genomes]
rs752767	0.93[EUR][1000 genomes]
rs896555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs896556	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1669884	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42720800-42844400	Weak transcription	Small Intestine	intestine
2	chr12:42816200-42858200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr12:42816800-42862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:42820000-42858200	Weak transcription	Gastric	stomach
5	chr12:42820200-42853000	Weak transcription	Fetal Heart	heart
6	chr12:42826400-42859000	Weak transcription	Fetal Brain Male	brain
7	chr12:42826600-42858200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:42831800-42876400	Weak transcription	Psoas Muscle	Psoas
9	chr12:42832800-42845000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:42834200-42859600	Weak transcription	Brain Substantia Nigra	brain
11	chr12:42836000-42875800	Weak transcription	Stomach Mucosa	stomach
12	chr12:42836600-42853000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:42836800-42853000	Weak transcription	Right Ventricle	heart
14	chr12:42836800-42858800	Weak transcription	Brain Angular Gyrus	brain
15	chr12:42837000-42845400	Weak transcription	Hela-S3	cervix
16	chr12:42837000-42853200	Weak transcription	NHEK	skin
17	chr12:42837000-42853800	Weak transcription	Lung	lung
18	chr12:42837000-42858000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:42837000-42858000	Weak transcription	Aorta	Aorta
20	chr12:42837000-42858200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:42837000-42868800	Weak transcription	Esophagus	oesophagus
22	chr12:42837200-42863200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr12:42837400-42848000	Weak transcription	HepG2	liver
24	chr12:42838000-42844400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:42838400-42858000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr12:42838600-42845200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:42838600-42850000	Weak transcription	HSMMtube	muscle
28	chr12:42838600-42853200	Weak transcription	Brain Anterior Caudate	brain
29	chr12:42838800-42844400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr12:42839000-42844400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:42839600-42844800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr12:42839600-42846000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:42839800-42853000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:42840000-42856400	Weak transcription	Fetal Intestine Small	intestine
35	chr12:42840400-42850200	Weak transcription	Left Ventricle	heart
36	chr12:42840400-42860800	Weak transcription	Colonic Mucosa	Colon
37	chr12:42840600-42844800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr12:42840600-42845200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:42840600-42852800	Weak transcription	Adipose Nuclei	Adipose
40	chr12:42840600-42858000	Weak transcription	Placenta	Placenta
41	chr12:42840600-42860000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr12:42840800-42846200	Weak transcription	Liver	Liver
43	chr12:42840800-42847200	Weak transcription	K562	blood
44	chr12:42840800-42849400	Enhancers	Primary B cells from peripheral blood	blood
45	chr12:42840800-42853200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr12:42840800-42853200	Weak transcription	Fetal Kidney	kidney
47	chr12:42840800-42858200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:42841000-42846400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr12:42841000-42849000	Enhancers	Primary B cells from cord blood	blood
50	chr12:42841000-42850200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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