Variant report

Variant	rs455032
Chromosome Location	chr1:75196488-75196489
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr1:75195465-75196660	SK-N-SH	brain:	n/a	chr1:75195864-75195872 chr1:75195863-75195873 chr1:75195864-75195873 chr1:75195862-75195874 chr1:75195863-75195872 chr1:75195862-75195873 chr1:75195864-75195871
2	GATA3	chr1:75195358-75196710	SK-N-SH	brain:	n/a	chr1:75195993-75196002 chr1:75195993-75196000 chr1:75195966-75195974 chr1:75195993-75196000 chr1:75195993-75196000 chr1:75195986-75196007
3	GATA3	chr1:75195434-75196539	SK-N-SH	brain:	n/a	chr1:75195993-75196002 chr1:75195993-75196000 chr1:75195966-75195974 chr1:75195993-75196000 chr1:75195993-75196000 chr1:75195986-75196007
4	GATA3	chr1:75195494-75196548	A549	lung:	n/a	chr1:75195993-75196002 chr1:75195993-75196000 chr1:75195966-75195974 chr1:75195993-75196000 chr1:75195993-75196000 chr1:75195986-75196007

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:75195743..75197778-chr1:75197921..75199580,2	MCF-7	breast:

Variant related genes	Relation type
TYW3	TF binding region
ENSG00000162623	Chromatin interaction
ENSG00000116791	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1051122	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10874122	0.92[ASN][1000 genomes]
rs10890142	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11485298	0.91[ASN][1000 genomes]
rs11485555	0.93[ASN][1000 genomes]
rs12410060	0.92[ASN][1000 genomes]
rs1248244	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1409785	0.91[ASN][1000 genomes]
rs1465483	0.97[ASN][1000 genomes]
rs1475396	0.91[ASN][1000 genomes]
rs1969111	0.87[ASN][1000 genomes]
rs1980851	0.87[ASN][1000 genomes]
rs277368	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277369	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277374	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277375	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277376	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277380	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs277396	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs277398	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277402	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2795030	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28482086	0.91[ASN][1000 genomes]
rs28568334	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28583318	0.91[ASN][1000 genomes]
rs2881153	0.91[ASN][1000 genomes]
rs28857918	0.93[ASN][1000 genomes]
rs28879157	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3806160	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3819946	0.91[ASN][1000 genomes]
rs3931020	0.92[ASN][1000 genomes]
rs405445	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4145871	0.91[ASN][1000 genomes]
rs438014	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs452242	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs525487	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7522428	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs968358	0.98[AMR][1000 genomes];1.00[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs455032	CRYZ	cis	Artery Tibial	GTEx
rs455032	CRYZ	cis	Adipose Subcutaneous	GTEx
rs455032	CRYZ	cis	Esophagus Mucosa	GTEx
rs455032	CRYZ	cis	Whole Blood	GTEx
rs455032	CRYZ	cis	Nerve Tibial	GTEx
rs455032	CRYZ	cis	lung	GTEx
rs455032	CRYZ	cis	multi-tissue	Pritchard
rs455032	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs455032	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75167000-75197200	Weak transcription	Right Ventricle	heart
2	chr1:75171000-75197200	Weak transcription	Brain Angular Gyrus	brain
3	chr1:75174800-75198000	Weak transcription	Thymus	Thymus
4	chr1:75180400-75197200	Weak transcription	Psoas Muscle	Psoas
5	chr1:75183000-75198400	Weak transcription	Fetal Brain Male	brain
6	chr1:75187400-75197200	Weak transcription	Stomach Mucosa	stomach
7	chr1:75187800-75197200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:75188200-75197200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:75188200-75198000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:75188400-75196800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr1:75188400-75197200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:75188400-75198000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:75189000-75197200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:75189400-75197200	Weak transcription	Left Ventricle	heart
15	chr1:75189400-75197400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:75189600-75197200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:75189600-75197400	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:75189800-75196800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:75191400-75197200	Weak transcription	Primary T cells from cord blood	blood
20	chr1:75192000-75197200	Weak transcription	Right Atrium	heart
21	chr1:75192200-75196600	Weak transcription	Aorta	Aorta
22	chr1:75192200-75197000	Weak transcription	Fetal Lung	lung
23	chr1:75192200-75197200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr1:75192200-75197200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:75192200-75197200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:75192200-75197200	Weak transcription	Colonic Mucosa	Colon
27	chr1:75192200-75197200	Weak transcription	Lung	lung
28	chr1:75192200-75197200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:75192200-75197400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:75192200-75197600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr1:75192200-75197800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:75192200-75198000	Weak transcription	Gastric	stomach
33	chr1:75192400-75197200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:75192400-75197200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:75192400-75197200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:75192400-75197200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:75192400-75197200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:75192400-75197200	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:75192400-75197400	Weak transcription	Spleen	Spleen
40	chr1:75192400-75198000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr1:75192400-75198000	Weak transcription	Fetal Thymus	thymus
42	chr1:75192600-75197600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:75192800-75197600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr1:75193000-75197200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:75193000-75197200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:75193200-75197200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr1:75193200-75197400	Weak transcription	Primary B cells from cord blood	blood
48	chr1:75194600-75198200	Weak transcription	Small Intestine	intestine
49	chr1:75194800-75196600	Enhancers	NHLF	lung
50	chr1:75194800-75196600	Enhancers	Osteobl	bone

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