Variant report

Variant	rs1424671
Chromosome Location	chr1:75189847-75189848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12129513	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2345438	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28535522	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28588069	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28602706	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28640981	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28683801	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28685856	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28767547	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28796389	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28796647	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28804435	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28831813	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35497701	1.00[ASN][1000 genomes]
rs3845356	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3845357	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3889133	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55895041	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790736	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790737	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790739	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749690	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv830259	chr1:75089177-75241062	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv871152	chr1:75152186-75197533	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
5	esv1851105	chr1:75152186-75302921	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1424671	CRYZ	cis	lung	GTEx
rs1424671	CRYZ	cis	multi-tissue	Pritchard
rs1424671	CRYZ	cis	Esophagus Mucosa	GTEx
rs1424671	CRYZ	cis	Adipose Subcutaneous	GTEx
rs1424671	TYW3	cis	Muscle Skeletal	GTEx
rs1424671	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs1424671	CRYZ	cis	Artery Aorta	GTEx
rs1424671	CRYZ	cis	Artery Tibial	GTEx
rs1424671	CRYZ	cis	Nerve Tibial	GTEx
rs1424671	CRYZ	cis	Whole Blood	GTEx
rs1424671	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75166400-75191400	Weak transcription	Placenta	Placenta
2	chr1:75166600-75194800	Weak transcription	Esophagus	oesophagus
3	chr1:75167000-75197200	Weak transcription	Right Ventricle	heart
4	chr1:75167600-75190600	Strong transcription	Liver	Liver
5	chr1:75167600-75190800	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:75167800-75190000	Strong transcription	Adipose Nuclei	Adipose
7	chr1:75169400-75190600	Strong transcription	Primary B cells from cord blood	blood
8	chr1:75169400-75191600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:75169800-75191800	Weak transcription	Colonic Mucosa	Colon
10	chr1:75171000-75197200	Weak transcription	Brain Angular Gyrus	brain
11	chr1:75174800-75198000	Weak transcription	Thymus	Thymus
12	chr1:75175400-75196000	Weak transcription	HSMMtube	muscle
13	chr1:75176800-75191600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:75177400-75191600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:75177400-75191600	Weak transcription	Gastric	stomach
16	chr1:75177400-75191800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:75178000-75191800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:75179400-75191200	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:75179600-75191200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:75179800-75191600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:75179800-75191600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:75180000-75191000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:75180000-75196000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:75180400-75191000	Strong transcription	A549	lung
25	chr1:75180400-75197200	Weak transcription	Psoas Muscle	Psoas
26	chr1:75180600-75191200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:75180800-75190800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:75180800-75190800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:75180800-75190800	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:75181400-75190600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:75181600-75190600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:75182200-75191000	Strong transcription	NHDF-Ad	bronchial
33	chr1:75183000-75198400	Weak transcription	Fetal Brain Male	brain
34	chr1:75183200-75190400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:75183600-75190600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:75183800-75194000	Weak transcription	Fetal Heart	heart
37	chr1:75184200-75190000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:75184400-75191600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr1:75184800-75191000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:75185000-75191600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:75185600-75190800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:75185800-75191000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:75186200-75191600	Weak transcription	Fetal Stomach	stomach
44	chr1:75186400-75190000	Strong transcription	Fetal Kidney	kidney
45	chr1:75187200-75191800	Weak transcription	Dnd41	blood
46	chr1:75187200-75195400	Weak transcription	HMEC	breast
47	chr1:75187400-75191600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:75187400-75197200	Weak transcription	Stomach Mucosa	stomach
49	chr1:75187600-75190400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:75187600-75191600	Weak transcription	Primary hematopoietic stem cells	blood

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