Variant report

Variant	rs670441
Chromosome Location	chr1:210469271-210469272
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210428073..210429613-chr1:210467774..210469897,2	MCF-7	breast:
2	chr1:210467132..210470101-chr1:210476675..210478835,2	MCF-7	breast:
3	chr1:210418192..210421005-chr1:210465903..210469381,6	MCF-7	breast:
4	chr1:210467411..210469958-chr1:210471110..210473541,2	K562	blood:
5	chr1:210468992..210470663-chr1:210546905..210548880,2	K562	blood:
6	chr1:210468377..210470093-chr1:210472227..210474687,2	MCF-7	breast:
7	chr1:210469230..210471169-chr1:210545852..210548678,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233455	Chromatin interaction
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1040563	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12739013	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12739023	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1338285	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4844990	0.89[AFR][1000 genomes]
rs655829	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs655847	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs656753	0.94[ASW][hapmap];0.80[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6658075	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs669189	0.96[AFR][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	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs670441	HHAT	cis	parietal	SCAN
rs670441	SERTAD4	cis	parietal	SCAN
rs670441	SYT14	cis	parietal	SCAN
rs670441	CAMK1G	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210465800-210470200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:210466400-210469400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:210466600-210469600	Enhancers	Rectal Smooth Muscle	rectum
4	chr1:210466600-210470000	Enhancers	Fetal Stomach	stomach
5	chr1:210466600-210474200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:210466800-210469400	Enhancers	Adipose Nuclei	Adipose
7	chr1:210466800-210469400	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr1:210466800-210477400	Enhancers	Fetal Muscle Leg	muscle
9	chr1:210467000-210469400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:210467000-210470000	Enhancers	Fetal Muscle Trunk	muscle
11	chr1:210467200-210469400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:210467200-210469400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:210467200-210469800	Enhancers	Fetal Heart	heart
14	chr1:210467200-210470000	Weak transcription	Fetal Kidney	kidney
15	chr1:210467800-210469400	Enhancers	Fetal Lung	lung
16	chr1:210467800-210469400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr1:210468000-210469400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:210468200-210475000	Weak transcription	Ovary	ovary
19	chr1:210468600-210473600	Weak transcription	Lung	lung
20	chr1:210468600-210474200	Weak transcription	Brain Substantia Nigra	brain
21	chr1:210468800-210470000	Weak transcription	Esophagus	oesophagus
22	chr1:210468800-210470000	Enhancers	Stomach Smooth Muscle	stomach
23	chr1:210468800-210470400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:210468800-210471600	Weak transcription	Left Ventricle	heart
25	chr1:210468800-210472400	Weak transcription	HMEC	breast
26	chr1:210468800-210473400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:210468800-210474200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:210468800-210474200	Weak transcription	Stomach Mucosa	stomach
29	chr1:210469000-210469800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:210469000-210470000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:210469000-210472600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:210469000-210474200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr1:210469000-210474400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:210469200-210470000	Enhancers	NHDF-Ad	bronchial
35	chr1:210469200-210470200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:210469200-210471400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:210469200-210471800	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:210469200-210472000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:210469200-210472400	Weak transcription	Placenta	Placenta
40	chr1:210469200-210473000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links