Variant report

Variant	rs10161
Chromosome Location	chr1:75232213-75232214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:75230355..75233919-chr1:75236315..75238196,3	K562	blood:
2	chr1:75197358..75200500-chr1:75231674..75234194,4	K562	blood:
3	chr1:71544757..71547243-chr1:75230448..75232270,2	K562	blood:
4	chr1:75226788..75230241-chr1:75231524..75234649,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FPGT-TNNI3K-5	chr1:75231968-75232362	NONHSAT003973

Variant related genes	Relation type
ENSG00000162623	Chromatin interaction
ENSG00000116791	Chromatin interaction
ENSG00000132485	Chromatin interaction
ENSG00000229956	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12125889	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12129513	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1574941	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1590639	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17618340	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2345438	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28535522	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28588069	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28594379	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28640981	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28804435	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35497701	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3845356	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3845357	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3889133	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55895041	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57880013	0.93[ASN][1000 genomes]
rs6668736	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10161	CRYZ	cis	Adipose Subcutaneous	GTEx
rs10161	CRYZ	cis	multi-tissue	Pritchard
rs10161	CRYZ	cis	lung	GTEx
rs10161	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs10161	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs10161	CRYZ	cis	Nerve Tibial	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75205200-75232400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:75206200-75232400	Weak transcription	Small Intestine	intestine
3	chr1:75206200-75232800	Weak transcription	NHLF	lung
4	chr1:75206800-75233600	Weak transcription	Gastric	stomach
5	chr1:75207600-75233400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:75216000-75235200	Weak transcription	Right Ventricle	heart
7	chr1:75219200-75233400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:75219800-75232400	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:75219800-75232600	Weak transcription	K562	blood
10	chr1:75221400-75232400	Weak transcription	NHEK	skin
11	chr1:75221400-75238000	Weak transcription	A549	lung
12	chr1:75221600-75234600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:75221600-75237600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr1:75222200-75236000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:75223000-75232600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:75223000-75232800	Weak transcription	Esophagus	oesophagus
17	chr1:75223000-75235200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:75223200-75232600	Weak transcription	Fetal Brain Female	brain
19	chr1:75223200-75232800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:75223200-75233400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:75223600-75232800	Weak transcription	Thymus	Thymus
22	chr1:75223600-75235200	Weak transcription	Spleen	Spleen
23	chr1:75223800-75232800	Weak transcription	HepG2	liver
24	chr1:75223800-75233600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:75224000-75232600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:75224200-75233000	Weak transcription	Fetal Lung	lung
27	chr1:75224600-75232800	Weak transcription	Osteobl	bone
28	chr1:75225000-75235000	Weak transcription	Fetal Kidney	kidney
29	chr1:75225600-75232800	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:75225800-75233600	Weak transcription	Ovary	ovary
31	chr1:75226000-75237600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:75226400-75232600	Weak transcription	Fetal Stomach	stomach
33	chr1:75227800-75232400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:75227800-75233200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:75227800-75235600	Weak transcription	HUVEC	blood vessel
36	chr1:75228000-75232600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr1:75228000-75234400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:75228000-75235200	Weak transcription	Left Ventricle	heart
39	chr1:75228000-75235800	Weak transcription	Aorta	Aorta
40	chr1:75228400-75235000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:75228600-75234200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:75228800-75234600	Weak transcription	HMEC	breast
43	chr1:75229800-75232600	Strong transcription	Primary T cells from cord blood	blood
44	chr1:75230000-75234400	Weak transcription	NH-A	brain
45	chr1:75230200-75234800	Weak transcription	GM12878-XiMat	blood
46	chr1:75230800-75232400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:75230800-75232400	Weak transcription	Placenta	Placenta
48	chr1:75230800-75233000	Weak transcription	Fetal Intestine Large	intestine
49	chr1:75230800-75238400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:75231000-75232600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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