Variant report

Variant	rs2347214
Chromosome Location	chr1:75841038-75841039
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:75826578..75828663-chr1:75838109..75841105,2	K562	blood:
2	chr1:75820905..75823291-chr1:75839784..75841753,2	K562	blood:
3	chr1:75837137..75838827-chr1:75839642..75842194,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1036950	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10747387	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10874264	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10874305	0.87[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs10874311	0.82[JPT][hapmap]
rs1107148	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1116878	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs12402118	0.84[CHD][hapmap]
rs1249784	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1249786	0.94[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1249794	0.81[CHD][hapmap]
rs12738260	0.82[JPT][hapmap]
rs1343519	0.87[CHB][hapmap];0.88[CHD][hapmap];0.88[ASN][1000 genomes]
rs1343520	0.80[CHB][hapmap];0.84[CHD][hapmap];0.81[MKK][hapmap];0.80[ASN][1000 genomes]
rs1858627	0.94[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap]
rs1858628	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1889036	0.83[JPT][hapmap]
rs1936358	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2587042	0.94[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6593575	0.94[CEU][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes]
rs6675276	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3368999	chr1:75524762-75933220	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1013952	chr1:75716654-75936048	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv535004	chr1:75716654-75936048	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1455	chr1:75812377-75864182	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv508304	chr1:75838772-75857426	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv435643	chr1:75840855-75848976	Active TSS Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2347214	CRYZ	cis	lymphoblastoid	seeQTL
rs2347214	SNORD45B	cis	cerebellum	SCAN
rs2347214	SLC44A5	cis	Muscle Skeletal	GTEx
rs2347214	TYW3	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75831400-75841400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:75833600-75841200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:75836800-75841200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:75837800-75841600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:75838200-75841800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:75840000-75841800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:75840400-75841200	Weak transcription	Placenta	Placenta
8	chr1:75840400-75841600	Active TSS	HepG2	liver
9	chr1:75840600-75841600	Active TSS	K562	blood
10	chr1:75840600-75841600	Active TSS	NHEK	skin
11	chr1:75840600-75842000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:75840800-75841200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr1:75841000-75841200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr1:75841000-75841400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr1:75841000-75841600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr1:75841000-75841600	Active TSS	Primary B cells from cord blood	blood
17	chr1:75841000-75841600	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr1:75841000-75841600	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr1:75841000-75841600	Active TSS	A549	lung
20	chr1:75841000-75841800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:75841000-75841800	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr1:75841000-75841800	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr1:75841000-75841800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:75841000-75841800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:75841000-75842000	Active TSS	H1 Cell Line	embryonic stem cell
26	chr1:75841000-75842000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:75841000-75842000	Active TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links