Variant report

Variant	rs55895041
Chromosome Location	chr1:75203382-75203383
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:75203296-75204035	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:75203151-75203761	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:75203325-75204003	Hela-S3	cervix:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:75197640..75200637-chr1:75200867..75204722,5	MCF-7	breast:
2	chr1:75197578..75200968-chr1:75201632..75206969,6	MCF-7	breast:
3	chr1:75200664..75203474-chr1:76250808..76253106,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FPGT-TNNI3K-4	chr1:75203106-75203390	NONHSAT003970

No data

Variant related genes	Relation type
CRYZ	TF binding region
ENSG00000162623	Chromatin interaction
ENSG00000137955	Chromatin interaction
ENSG00000206620	Chromatin interaction
ENSG00000116791	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10161	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12125889	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12129513	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1424671	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1574941	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1590639	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17618340	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2345438	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535522	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28594379	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28602706	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28640981	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654603	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28683801	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28685856	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695657	1.00[ASN][1000 genomes]
rs28796389	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28796647	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28804435	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831813	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35497701	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3889133	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790736	1.00[ASN][1000 genomes]
rs61790737	1.00[ASN][1000 genomes]
rs61790739	1.00[ASN][1000 genomes]
rs6668736	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs749690	1.00[ASN][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
rs55895041	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs55895041	CRYZ	cis	multi-tissue	Pritchard
rs55895041	CRYZ	cis	Adipose Subcutaneous	GTEx
rs55895041	CRYZ	cis	lung	GTEx
rs55895041	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs55895041	CRYZ	cis	Nerve Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75199400-75203400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:75199400-75203800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:75199600-75206000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:75199800-75207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:75200000-75231600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:75200200-75203400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:75200200-75205200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:75200200-75217600	Weak transcription	Stomach Mucosa	stomach
9	chr1:75200400-75203600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:75200400-75210600	Weak transcription	Colonic Mucosa	Colon
11	chr1:75200400-75218400	Weak transcription	Fetal Heart	heart
12	chr1:75200800-75203600	Weak transcription	Psoas Muscle	Psoas
13	chr1:75201000-75206000	Strong transcription	Fetal Lung	lung
14	chr1:75201200-75206200	Strong transcription	HSMM	muscle
15	chr1:75201200-75210600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:75201200-75212400	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:75201400-75212800	Strong transcription	Primary B cells from cord blood	blood
18	chr1:75201400-75231800	Strong transcription	Dnd41	blood
19	chr1:75201600-75206200	Strong transcription	HUVEC	blood vessel
20	chr1:75202000-75208600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:75202200-75204200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr1:75202200-75205000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:75202200-75207400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:75202200-75207800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:75202200-75209000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:75202400-75203800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:75202400-75204000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:75202400-75204000	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr1:75202400-75204400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:75202400-75204400	Strong transcription	NHEK	skin
31	chr1:75202400-75204600	Strong transcription	Brain Anterior Caudate	brain
32	chr1:75202400-75205400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:75202400-75205600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:75202400-75205800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr1:75202400-75206200	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:75202400-75206200	Strong transcription	HSMMtube	muscle
37	chr1:75202400-75206400	Strong transcription	Brain Angular Gyrus	brain
38	chr1:75202400-75206600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:75202400-75207800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:75202400-75208000	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:75202400-75208000	Strong transcription	K562	blood
42	chr1:75202400-75208400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr1:75202400-75208600	Strong transcription	Brain Substantia Nigra	brain
44	chr1:75202400-75209600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:75202400-75210000	Strong transcription	Fetal Thymus	thymus
46	chr1:75202400-75211400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr1:75202400-75212200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:75202400-75212800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:75202400-75212800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:75202400-75213000	Strong transcription	Liver	Liver

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