Variant report

Variant	rs28602706
Chromosome Location	chr1:75199973-75199974
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:33)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:33 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:75199840-75199990	HBMEC	blood vessel:	n/a	n/a
2	POLR2A	chr1:75198636-75200123	IMR90	lung:	n/a	n/a
3	FOS	chr1:75199409-75200096	MCF10A-Er-Src	breast:	n/a	n/a
4	CTCF	chr1:75199840-75199990	HRPEpiC	eye:	n/a	n/a
5	BACH1	chr1:75199266-75200027	K562	blood:	n/a	n/a
6	POLR2A	chr1:75199857-75200057	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr1:75199860-75200054	K562	blood:	n/a	n/a
8	GATA1	chr1:75198495-75200354	PBDE	blood:	n/a	chr1:75198538-75198548
9	CTCF	chr1:75199840-75199990	GM06990	blood:	n/a	n/a
10	POLR2A	chr1:75196850-75200950	GM12878	blood:	n/a	n/a
11	MXI1	chr1:75198369-75200177	IMR90	lung:	n/a	n/a
12	POLR2A	chr1:75198481-75200318	K562	blood:	n/a	n/a
13	POLR2A	chr1:75196987-75201662	GM12891	blood:	n/a	n/a
14	RELA	chr1:75197115-75200040	GM18505	blood:	n/a	n/a
15	WRNIP1	chr1:75199850-75200046	GM12878	blood:	n/a	n/a
16	JUN	chr1:75198636-75200033	K562	blood:	n/a	n/a
17	CTCF	chr1:75198462-75200591	SK-N-SH	brain:	n/a	chr1:75198476-75198485
18	CTCF	chr1:75199900-75200050	BE2_C	brain:	n/a	n/a
19	CTCF	chr1:75199940-75200090	HEEpiC	esophagus:	n/a	n/a
20	TBP	chr1:75198445-75200029	K562	blood:	n/a	n/a
21	FOS	chr1:75199360-75200048	MCF10A-Er-Src	breast:	n/a	n/a
22	CTCF	chr1:75199960-75200110	GM12872	blood:	n/a	n/a
23	CTCF	chr1:75199920-75200070	SAEC	small airway:	n/a	n/a
24	GATA2	chr1:75198800-75200466	HUVEC	blood vessel:	n/a	n/a
25	CTCF	chr1:75199840-75199990	HPAF	blood vessel:	n/a	n/a
26	TBL1XR1	chr1:75198574-75200003	K562	blood:	n/a	n/a
27	JUND	chr1:75198559-75200203	K562	blood:	n/a	n/a
28	MXI1	chr1:75198136-75200124	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr1:75197016-75200333	GM12878	blood:	n/a	n/a
30	GATA2	chr1:75199839-75200155	SH-SY5Y	brain:	n/a	n/a
31	CTCF	chr1:75199880-75200030	SAEC	small airway:	n/a	n/a
32	RAD21	chr1:75198292-75199974	SK-N-SH	brain:	n/a	chr1:75198865-75198875
33	CHD1	chr1:75198398-75200023	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:75197640..75200637-chr1:75200867..75204722,5	MCF-7	breast:
2	chr1:75182455..75184516-chr1:75199218..75200932,2	K562	blood:
3	chr1:75197237..75200127-chr1:76254006..76255529,2	K562	blood:
4	chr1:75197578..75200968-chr1:75201632..75206969,6	MCF-7	breast:
5	chr1:74977554..74979985-chr1:75198825..75201036,2	K562	blood:
6	chr1:74969628..74970367-chr1:75199475..75200023,2	MCF-7	breast:

No data

Variant related genes	Relation type
CRYZ	TF binding region
TYW3	TF binding region
ENSG00000162623	Chromatin interaction
ENSG00000162621	Chromatin interaction
ENSG00000201487	Chromatin interaction

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]
rs1424671	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][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	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28640981	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654603	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28683801	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28685856	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695657	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28767547	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28796389	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28796647	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28804435	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831813	0.92[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	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3845357	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3889133	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55895041	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790736	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790737	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790739	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749690	0.88[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	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
5	nsv546579	chr1:75197533-75200486	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs28602706	CRYZ	cis	Artery Tibial	GTEx
rs28602706	CRYZ	cis	Nerve Tibial	GTEx
rs28602706	CRYZ	cis	Artery Aorta	GTEx
rs28602706	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs28602706	TYW3	cis	Muscle Skeletal	GTEx
rs28602706	CRYZ	cis	multi-tissue	Pritchard
rs28602706	CRYZ	cis	Adipose Subcutaneous	GTEx
rs28602706	CRYZ	cis	lung	GTEx
rs28602706	CRYZ	cis	Whole Blood	GTEx
rs28602706	CRYZ	cis	Esophagus Mucosa	GTEx
rs28602706	CRYZ	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75195600-75200400	Active TSS	A549	lung
2	chr1:75196800-75200000	Active TSS	Fetal Intestine Large	intestine
3	chr1:75197200-75200000	Active TSS	Right Atrium	heart
4	chr1:75197200-75200400	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:75197400-75200000	Active TSS	Osteobl	bone
6	chr1:75197600-75200000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:75197600-75200000	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr1:75197600-75200000	Active TSS	Muscle Satellite Cultured Cells	--
9	chr1:75197600-75200000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:75197600-75200200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:75197600-75200200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:75197600-75200200	Active TSS	Ovary	ovary
13	chr1:75197600-75200400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:75197600-75200600	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr1:75197800-75200000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:75197800-75200000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:75197800-75200200	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr1:75197800-75200200	Active TSS	NHDF-Ad	bronchial
19	chr1:75197800-75200800	Active TSS	NHLF	lung
20	chr1:75197800-75201800	Active TSS	GM12878-XiMat	blood
21	chr1:75198000-75200000	Active TSS	H1 Cell Line	embryonic stem cell
22	chr1:75198000-75200000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr1:75198000-75200000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:75198000-75200000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:75198000-75200000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:75198000-75200000	Active TSS	Brain Germinal Matrix	brain
27	chr1:75198000-75200000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:75198000-75200000	Active TSS	HMEC	breast
29	chr1:75198000-75200000	Active TSS	K562	blood
30	chr1:75198000-75200200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:75198000-75200200	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr1:75198000-75200600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:75198200-75200000	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr1:75198200-75200000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:75198200-75200000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:75198200-75200000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:75198200-75200000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:75198200-75200000	Active TSS	Psoas Muscle	Psoas
39	chr1:75198600-75200000	Active TSS	Fetal Muscle Trunk	muscle
40	chr1:75199200-75200000	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr1:75199200-75203000	Weak transcription	Spleen	Spleen
42	chr1:75199400-75200000	Weak transcription	Small Intestine	intestine
43	chr1:75199400-75200000	Active TSS	Stomach Smooth Muscle	stomach
44	chr1:75199400-75200200	Flanking Active TSS	Primary T cells from cord blood	blood
45	chr1:75199400-75200200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:75199400-75200400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:75199400-75203000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:75199400-75203000	Weak transcription	Lung	lung
49	chr1:75199400-75203400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:75199400-75203800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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