Variant report

Variant	rs4768412
Chromosome Location	chr12:42869140-42869141
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42867148..42869187-chr12:42983143..42985743,2	K562	blood:

Variant related genes	Relation type
ENSG00000139174	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1043652	0.96[CEU][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1043656	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880282	0.81[EUR][1000 genomes]
rs10880284	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs11181421	0.83[EUR][1000 genomes]
rs11181427	0.88[EUR][1000 genomes]
rs11181453	0.88[EUR][1000 genomes]
rs11181461	0.82[JPT][hapmap];0.91[MEX][hapmap]
rs11181484	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12229224	0.86[EUR][1000 genomes]
rs12229266	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12230583	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12231335	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12422938	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423383	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs12425945	0.92[CEU][hapmap]
rs12578312	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs1376931	0.92[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs1629725	0.89[EUR][1000 genomes]
rs1669884	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1669888	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1669890	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1669891	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1669894	0.89[EUR][1000 genomes]
rs1669895	0.89[EUR][1000 genomes]
rs1669897	0.89[EUR][1000 genomes]
rs1669898	0.89[EUR][1000 genomes]
rs1669899	0.88[EUR][1000 genomes]
rs1669900	0.89[EUR][1000 genomes]
rs1669901	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1669903	0.92[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1669905	0.89[EUR][1000 genomes]
rs1669911	0.88[EUR][1000 genomes]
rs1669912	0.89[EUR][1000 genomes]
rs1669913	0.89[EUR][1000 genomes]
rs1669914	0.89[EUR][1000 genomes]
rs1669935	0.89[EUR][1000 genomes]
rs1669937	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs1796354	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1796355	0.89[EUR][1000 genomes]
rs1796356	0.89[EUR][1000 genomes]
rs1796357	0.92[CEU][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1796359	0.89[EUR][1000 genomes]
rs1796360	0.89[EUR][1000 genomes]
rs1796365	0.89[EUR][1000 genomes]
rs1796373	0.89[EUR][1000 genomes]
rs1796374	0.89[EUR][1000 genomes]
rs1796377	0.89[EUR][1000 genomes]
rs1796379	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1796385	0.89[EUR][1000 genomes]
rs1796387	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1796389	0.92[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1796392	0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1796395	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1796396	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1796397	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1796398	0.92[CEU][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2053946	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2243465	0.92[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs2406872	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2406969	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2600911	0.89[EUR][1000 genomes]
rs2600912	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2600916	0.89[EUR][1000 genomes]
rs2600917	0.82[EUR][1000 genomes]
rs2600918	0.89[EUR][1000 genomes]
rs2708063	0.89[EUR][1000 genomes]
rs2708069	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2708075	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2708077	0.82[EUR][1000 genomes]
rs2708506	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2952653	0.89[EUR][1000 genomes]
rs3213989	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3747563	0.91[EUR][1000 genomes]
rs3761677	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs3827524	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4603368	0.87[EUR][1000 genomes]
rs4768397	0.87[CEU][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs4768398	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs4768401	0.92[CEU][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs7134895	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs721447	0.88[EUR][1000 genomes]
rs73122408	0.89[EUR][1000 genomes]
rs73122414	0.88[EUR][1000 genomes]
rs73122418	0.89[EUR][1000 genomes]
rs752767	0.89[EUR][1000 genomes]
rs896555	0.92[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs896556	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4768412	HSD17B6	trans	cerebellum	SCAN
rs4768412	KIF21A	cis	parietal	SCAN
rs4768412	NELL2	cis	parietal	SCAN
rs4768412	CPNE8	cis	parietal	SCAN
rs4768412	PPHLN1	cis	Artery Tibial	GTEx
rs4768412	KIF21A	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42831800-42876400	Weak transcription	Psoas Muscle	Psoas
2	chr12:42836000-42875800	Weak transcription	Stomach Mucosa	stomach
3	chr12:42853400-42869200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:42860200-42870400	Weak transcription	Pancreas	Pancrea
5	chr12:42860200-42876200	Weak transcription	Gastric	stomach
6	chr12:42861400-42876000	Weak transcription	Lung	lung
7	chr12:42862800-42876000	Weak transcription	Aorta	Aorta
8	chr12:42863400-42869200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:42863400-42869600	Enhancers	Fetal Heart	heart
10	chr12:42863400-42874200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:42863400-42875600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:42863400-42876000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:42864400-42876000	Weak transcription	Spleen	Spleen
14	chr12:42864800-42875600	Weak transcription	Fetal Stomach	stomach
15	chr12:42865000-42869200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr12:42865600-42869200	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr12:42866200-42869200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:42866200-42869200	Enhancers	NHDF-Ad	bronchial
19	chr12:42866200-42869800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:42866200-42876000	Enhancers	Primary B cells from peripheral blood	blood
21	chr12:42866400-42869400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr12:42866600-42869200	Enhancers	HSMMtube	muscle
23	chr12:42866600-42869400	Enhancers	Osteobl	bone
24	chr12:42866600-42869600	Enhancers	NHEK	skin
25	chr12:42866600-42870800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:42866800-42869600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:42867000-42875800	Weak transcription	Right Atrium	heart
28	chr12:42867200-42869400	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr12:42867200-42874600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:42867200-42875800	Weak transcription	Ovary	ovary
31	chr12:42867400-42869200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:42867400-42869400	Enhancers	NHLF	lung
33	chr12:42867400-42872200	Weak transcription	Fetal Lung	lung
34	chr12:42867400-42873200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:42867400-42874600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:42867800-42869600	Enhancers	HUVEC	blood vessel
37	chr12:42868000-42869200	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr12:42868000-42869200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:42868000-42869400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:42868000-42869400	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr12:42868000-42869400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr12:42868200-42869200	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr12:42868200-42869400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:42868200-42869600	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr12:42868400-42869400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:42868400-42869600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:42868600-42869200	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr12:42868600-42869200	Flanking Active TSS	HMEC	breast
49	chr12:42868600-42869600	Enhancers	NH-A	brain
50	chr12:42868600-42869800	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links