Variant report

Variant	rs12434478
Chromosome Location	chr14:69435983-69435984
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:69420750..69423419-chr14:69434981..69437135,2	K562	blood:
2	chr14:69415039..69417585-chr14:69434781..69436421,2	K562	blood:
3	chr14:69431359..69433978-chr14:69434741..69437243,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1007407	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs10083451	0.85[JPT][hapmap]
rs10137547	0.90[ASN][1000 genomes]
rs10139873	0.85[JPT][hapmap]
rs10145565	0.85[JPT][hapmap]
rs10147976	0.90[ASN][1000 genomes]
rs11158782	0.85[JPT][hapmap]
rs11158790	0.85[JPT][hapmap]
rs1147481	0.85[JPT][hapmap]
rs12432970	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12589028	0.85[JPT][hapmap]
rs1275407	0.85[JPT][hapmap]
rs17093668	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17106670	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001998	0.85[JPT][hapmap]
rs2012750	0.90[ASN][1000 genomes]
rs2012764	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2012785	0.90[ASN][1000 genomes]
rs2024892	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2024893	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2268968	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[ASN][1000 genomes]
rs2300875	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs28561965	0.90[ASN][1000 genomes]
rs28613298	0.85[JPT][hapmap]
rs4243632	0.87[ASN][1000 genomes]
rs4902682	0.85[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6573869	0.85[JPT][hapmap]
rs7140693	0.88[CHD][hapmap]
rs7146225	0.85[JPT][hapmap]
rs7149487	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7160629	0.85[JPT][hapmap]
rs72733548	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8015876	1.00[JPT][hapmap]
rs9323524	0.85[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832823	chr14:69388853-69567638	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12434478	SMOC1	cis	cerebellum	SCAN
rs12434478	PLEKHG3	cis	cerebellum	SCAN
rs12434478	ADAM21	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69411200-69442600	Weak transcription	Fetal Brain Female	brain
2	chr14:69420200-69437200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr14:69420200-69441200	Genic enhancers	NHEK	skin
4	chr14:69420600-69441600	Genic enhancers	NH-A	brain
5	chr14:69421200-69442200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr14:69426000-69436600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr14:69426200-69436400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr14:69426200-69436600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr14:69426200-69436800	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr14:69427600-69437600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr14:69427600-69437600	Enhancers	Left Ventricle	heart
12	chr14:69428400-69437200	Enhancers	Adipose Nuclei	Adipose
13	chr14:69428400-69437200	Genic enhancers	NHLF	lung
14	chr14:69428400-69442200	Genic enhancers	Fetal Stomach	stomach
15	chr14:69428600-69439800	Genic enhancers	Fetal Intestine Small	intestine
16	chr14:69428600-69443400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr14:69429000-69436200	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr14:69429200-69439600	Enhancers	Fetal Thymus	thymus
19	chr14:69429400-69443800	Weak transcription	Brain Germinal Matrix	brain
20	chr14:69429800-69441400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr14:69429800-69442400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr14:69430000-69436200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr14:69430000-69437800	Enhancers	Fetal Intestine Large	intestine
24	chr14:69430000-69438000	Enhancers	Liver	Liver
25	chr14:69430000-69440400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:69430000-69441600	Genic enhancers	HSMM	muscle
27	chr14:69430200-69438800	Enhancers	Fetal Heart	heart
28	chr14:69430600-69437800	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr14:69430800-69436200	Enhancers	Brain Anterior Caudate	brain
30	chr14:69430800-69437600	Enhancers	Right Atrium	heart
31	chr14:69430800-69438200	Enhancers	Pancreas	Pancrea
32	chr14:69430800-69439000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr14:69431000-69438200	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr14:69431200-69436200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr14:69431600-69436000	Weak transcription	Fetal Brain Male	brain
36	chr14:69431600-69437400	Enhancers	Colonic Mucosa	Colon
37	chr14:69431800-69438400	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr14:69431800-69439200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr14:69431800-69444000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
40	chr14:69432000-69442400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr14:69432400-69436000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr14:69432400-69436200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr14:69432400-69437000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr14:69432400-69437600	Weak transcription	Hela-S3	cervix
45	chr14:69432400-69441400	Genic enhancers	HepG2	liver
46	chr14:69432600-69436000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr14:69432600-69438200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr14:69432600-69442200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr14:69432600-69443000	Weak transcription	Brain Substantia Nigra	brain
50	chr14:69432800-69436200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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