Variant report

Variant	rs6427297
Chromosome Location	chr1:155975493-155975494
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	chr1:155974280..155976413-chr1:155989519..155992083,2	MCF-7	breast:
2	chr1:155959078..155960932-chr1:155973199..155976085,2	K562	blood:

Variant related genes	Relation type
ENSG00000116584	Chromatin interaction
ENSG00000163479	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10796955	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs1111102	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264426	0.81[CEU][hapmap]
rs11486142	0.86[AMR][1000 genomes]
rs11585845	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs12037177	0.81[TSI][hapmap]
rs12118795	0.90[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap]
rs1889532	0.81[CEU][hapmap]
rs2282301	0.81[TSI][hapmap]
rs2297649	0.81[TSI][hapmap]
rs3820592	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4661218	0.81[CEU][hapmap]
rs59781317	0.88[AMR][1000 genomes]
rs6667652	0.81[TSI][hapmap]
rs6670493	0.80[CEU][hapmap]
rs72708238	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72708239	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7534858	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs915178	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs928596	0.81[CEU][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	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6427297	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs6427297	RORC	cis	cerebellum	SCAN
rs6427297	SNX27	cis	parietal	SCAN
rs6427297	ROBLD3	cis	parietal	SCAN
rs6427297	RIT1	cis	cerebellum	SCAN
rs6427297	YY1AP1	cis	cerebellum	SCAN
rs6427297	PRUNE	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155959200-155978200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:155959400-155976600	Weak transcription	Aorta	Aorta
3	chr1:155966200-155976600	Weak transcription	Brain Substantia Nigra	brain
4	chr1:155966200-155976800	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:155966400-155978200	Weak transcription	Left Ventricle	heart
6	chr1:155966400-155978400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:155967000-155976600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:155967000-155976600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:155967000-155978400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:155970800-155978200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:155971400-155978600	Weak transcription	Brain Angular Gyrus	brain
12	chr1:155971400-155978600	Weak transcription	NHDF-Ad	bronchial
13	chr1:155971600-155978400	Weak transcription	Ovary	ovary
14	chr1:155971600-155978400	Weak transcription	Right Ventricle	heart
15	chr1:155971600-155978600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr1:155971800-155976600	Weak transcription	Placenta	Placenta
17	chr1:155971800-155976600	Weak transcription	Pancreas	Pancrea
18	chr1:155971800-155976800	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:155971800-155978400	Weak transcription	Osteobl	bone
20	chr1:155971800-155978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:155972000-155976600	Weak transcription	Liver	Liver
22	chr1:155972000-155976600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr1:155972000-155978600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:155972200-155976600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr1:155972200-155976600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:155972200-155976800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:155972400-155976800	Weak transcription	Adipose Nuclei	Adipose
28	chr1:155972400-155978400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:155972400-155978400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:155972400-155978400	Weak transcription	Fetal Kidney	kidney
31	chr1:155972400-155978600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:155972600-155976200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:155972600-155976600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:155972800-155976600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:155972800-155978400	Weak transcription	HSMMtube	muscle
36	chr1:155973400-155976600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:155973400-155978200	Weak transcription	Esophagus	oesophagus
38	chr1:155973400-155978400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:155973400-155978400	Weak transcription	HSMM	muscle
40	chr1:155973600-155976000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:155973600-155976000	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr1:155973600-155978600	Weak transcription	NH-A	brain
43	chr1:155973800-155975600	Enhancers	HepG2	liver
44	chr1:155973800-155976000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:155973800-155976000	Weak transcription	Fetal Stomach	stomach
46	chr1:155973800-155976200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:155973800-155976600	Weak transcription	Fetal Lung	lung
48	chr1:155973800-155978200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:155973800-155978400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:155973800-155978400	Weak transcription	Small Intestine	intestine

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