Variant report

Variant	rs12435914
Chromosome Location	chr14:68911269-68911270
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:68887949..68890328-chr14:68911065..68913436,2	MCF-7	breast:
2	chr14:68909488..68911402-chr14:68914118..68916911,2	MCF-7	breast:
3	chr14:68771399..68773960-chr14:68910018..68913627,3	MCF-7	breast:
4	chr14:68910903..68913112-chr14:69019388..69021979,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258477	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10130683	0.88[ASN][1000 genomes]
rs10133813	0.82[JPT][hapmap]
rs10138140	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10139107	0.82[JPT][hapmap]
rs10146058	0.82[JPT][hapmap]
rs10149340	0.82[ASN][1000 genomes]
rs10467820	0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs12587397	0.82[JPT][hapmap]
rs12886429	0.82[JPT][hapmap]
rs12886864	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs1468279	0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs17105561	0.81[JPT][hapmap]
rs17105571	0.82[CEU][hapmap]
rs2040783	0.87[ASN][1000 genomes]
rs2074562	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2074563	0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2074564	0.89[ASN][1000 genomes]
rs2074565	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2093202	0.89[ASN][1000 genomes]
rs2097800	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2107340	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2717217	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2753404	0.82[JPT][hapmap]
rs2842322	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3784124	0.89[ASN][1000 genomes]
rs4411448	0.87[ASN][1000 genomes]
rs4902579	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4902583	0.81[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes]
rs4902594	0.81[ASN][1000 genomes]
rs4902595	0.82[JPT][hapmap]
rs5004090	0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs61986936	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6573837	0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs765899	0.84[MKK][hapmap]
rs9323512	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	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12435914	FAM71D	cis	parietal	SCAN
rs12435914	ACTN1	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68895200-68914400	Weak transcription	A549	lung
2	chr14:68906200-68911400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr14:68906200-68912200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr14:68906400-68911400	Weak transcription	Fetal Lung	lung
5	chr14:68906400-68912000	Enhancers	NHDF-Ad	bronchial
6	chr14:68906800-68916000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr14:68908000-68913000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr14:68908600-68912200	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr14:68908600-68917400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr14:68909000-68912600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr14:68909000-68916200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr14:68909200-68912000	Enhancers	Fetal Muscle Leg	muscle
13	chr14:68909600-68912000	Enhancers	Ovary	ovary
14	chr14:68909600-68912000	Enhancers	Psoas Muscle	Psoas
15	chr14:68909600-68912000	Enhancers	HMEC	breast
16	chr14:68909600-68912200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr14:68909600-68912200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr14:68909600-68912200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr14:68909600-68912200	Enhancers	HSMMtube	muscle
20	chr14:68909600-68912200	Enhancers	Osteobl	bone
21	chr14:68909600-68912600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr14:68909600-68912800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr14:68909600-68915000	Enhancers	Dnd41	blood
24	chr14:68909800-68912400	Enhancers	HSMM	muscle
25	chr14:68910000-68911400	Weak transcription	NHLF	lung
26	chr14:68910000-68912000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr14:68910000-68912000	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr14:68910400-68912000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr14:68910600-68912200	Enhancers	Adipose Nuclei	Adipose
30	chr14:68910800-68911400	Enhancers	H9 Cell Line	embryonic stem cell
31	chr14:68910800-68911800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr14:68910800-68911800	Enhancers	Fetal Muscle Trunk	muscle
33	chr14:68910800-68911800	Enhancers	NH-A	brain
34	chr14:68910800-68912000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr14:68910800-68912000	Enhancers	Fetal Thymus	thymus
36	chr14:68910800-68912000	Enhancers	Pancreas	Pancrea
37	chr14:68910800-68912200	Enhancers	Colon Smooth Muscle	Colon
38	chr14:68911000-68911400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr14:68911000-68911800	Enhancers	Brain Anterior Caudate	brain
40	chr14:68911000-68912200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr14:68911000-68912200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr14:68911200-68911800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr14:68911200-68911800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr14:68911200-68911800	Enhancers	Duodenum Mucosa	Duodenum
45	chr14:68911200-68911800	Enhancers	Lung	lung
46	chr14:68911200-68911800	Enhancers	Right Atrium	heart
47	chr14:68911200-68911800	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr14:68911200-68912000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr14:68911200-68912000	Enhancers	Liver	Liver
50	chr14:68911200-68912000	Enhancers	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links