Variant report

Variant	rs28695657
Chromosome Location	chr1:75197614-75197615
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:93)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:93 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr1:75197041-75197636	A549	lung:	n/a	n/a
2	CUX1	chr1:75196910-75198287	GM12878	blood:	n/a	n/a
3	CHD2	chr1:75197213-75198218	GM12878	blood:	n/a	n/a
4	TCF12	chr1:75196978-75197686	A549	lung:	n/a	n/a
5	HEY1	chr1:75197075-75198245	HepG2	liver:	n/a	n/a
6	RELA	chr1:75196976-75199695	GM19193	blood:	n/a	n/a
7	ARID3A	chr1:75196807-75197673	HepG2	liver:	n/a	n/a
8	EP300	chr1:75197593-75198249	GM12878	blood:	n/a	chr1:75198210-75198226
9	RELA	chr1:75197065-75199714	GM15510	blood:	n/a	n/a
10	TCF12	chr1:75197534-75198290	GM12878	blood:	n/a	n/a
11	NFIC	chr1:75197433-75198264	GM12878	blood:	n/a	n/a
12	GATA3	chr1:75196807-75197658	A549	lung:	n/a	chr1:75197228-75197244
13	ZBTB7A	chr1:75197506-75197684	HepG2	liver:	n/a	n/a
14	FOXM1	chr1:75197367-75198339	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:75197076-75197727	HepG2	liver:	n/a	n/a
16	ATF2	chr1:75196957-75197766	GM12878	blood:	n/a	n/a
17	RELA	chr1:75197077-75199725	GM12891	blood:	n/a	n/a
18	ZEB1	chr1:75197553-75197951	GM12878	blood:	n/a	n/a
19	HEY1	chr1:75196948-75198153	HepG2	liver:	n/a	n/a
20	RELA	chr1:75196990-75199882	GM12878	blood:	n/a	n/a
21	MTA3	chr1:75197225-75199820	GM12878	blood:	n/a	n/a
22	RELA	chr1:75197016-75199699	GM19099	blood:	n/a	n/a
23	POLR2A	chr1:75197570-75198297	GM12892	blood:	n/a	n/a
24	POLR2A	chr1:75196850-75200950	GM12878	blood:	n/a	n/a
25	EBF1	chr1:75197606-75198573	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:75196955-75199695	HepG2	liver:	n/a	n/a
27	POU2F2	chr1:75197580-75198259	GM12891	blood:	n/a	n/a
28	TEAD4	chr1:75196907-75197767	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:75196987-75201662	GM12891	blood:	n/a	n/a
30	POLR2A	chr1:75197017-75197718	HepG2	liver:	n/a	n/a
31	RELA	chr1:75197115-75200040	GM18505	blood:	n/a	n/a
32	NFIC	chr1:75196996-75197747	HepG2	liver:	n/a	n/a
33	CEBPB	chr1:75197224-75197716	HepG2	liver:	n/a	n/a
34	POLR2A	chr1:75197128-75198271	GM12891	blood:	n/a	n/a
35	NFIC	chr1:75197115-75197665	HepG2	liver:	n/a	n/a
36	GATA3	chr1:75196780-75197754	SK-N-SH	brain:	n/a	chr1:75197228-75197244
37	PAX5	chr1:75197505-75199249	GM12878	blood:	n/a	n/a
38	MXI1	chr1:75197095-75197656	HepG2	liver:	n/a	n/a
39	MYBL2	chr1:75197049-75197691	HepG2	liver:	n/a	n/a
40	POU2F2	chr1:75197575-75198279	GM12878	blood:	n/a	n/a
41	SP1	chr1:75197516-75198246	GM12878	blood:	n/a	n/a
42	ZNF384	chr1:75196761-75197618	GM12878	blood:	n/a	n/a
43	FOXA1	chr1:75197252-75197763	HepG2	liver:	n/a	n/a
44	EP300	chr1:75197323-75197677	HepG2	liver:	n/a	n/a
45	POLR2A	chr1:75197004-75197790	HepG2	liver:	n/a	n/a
46	FOSL2	chr1:75196855-75197684	A549	lung:	n/a	chr1:75197135-75197144 chr1:75197136-75197144 chr1:75197136-75197143
47	RELA	chr1:75196917-75199189	GM18526	blood:	n/a	n/a
48	POLR2A	chr1:75197396-75198248	GM12892	blood:	n/a	n/a
49	SP1	chr1:75196927-75197693	A549	lung:	n/a	n/a
50	FOXA2	chr1:75197349-75197677	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:75195743..75197778-chr1:75197921..75199580,2	MCF-7	breast:
2	chr1:75197237..75200127-chr1:76254006..76255529,2	K562	blood:
3	chr1:75197578..75200968-chr1:75201632..75206969,6	MCF-7	breast:

No data

Variant related genes	Relation type
TYW3	TF binding region
ENSG00000116791	Chromatin interaction
ENSG00000162623	Chromatin interaction
ENSG00000201487	Chromatin interaction

Extended variants
information (count: 30 )
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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28602706	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28640981	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28654603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28683801	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28685856	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28767547	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28796389	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28796647	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.97[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];0.93[EUR][1000 genomes]
rs3845357	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3889133	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55895041	1.00[ASN][1000 genomes]
rs61790736	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790737	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790739	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749690	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv1838134	chr1:75197533-75198602	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
6	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
rs28695657	CRYZ	cis	Adipose Subcutaneous	GTEx
rs28695657	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs28695657	CRYZ	cis	lung	GTEx
rs28695657	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs28695657	CRYZ	cis	Whole Blood	GTEx
rs28695657	CRYZ	cis	multi-tissue	Pritchard
rs28695657	CRYZ	cis	Artery Aorta	GTEx
rs28695657	CRYZ	cis	Esophagus Mucosa	GTEx
rs28695657	CRYZ	cis	Nerve Tibial	GTEx
rs28695657	CRYZ	cis	Artery Tibial	GTEx
rs28695657	TYW3	cis	Muscle Skeletal	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75174800-75198000	Weak transcription	Thymus	Thymus
2	chr1:75183000-75198400	Weak transcription	Fetal Brain Male	brain
3	chr1:75188200-75198000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:75188400-75198000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:75192200-75197800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:75192200-75198000	Weak transcription	Gastric	stomach
7	chr1:75192400-75198000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:75192400-75198000	Weak transcription	Fetal Thymus	thymus
9	chr1:75194600-75198200	Weak transcription	Small Intestine	intestine
10	chr1:75194800-75198000	Weak transcription	Brain Substantia Nigra	brain
11	chr1:75194800-75198200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:75195000-75198000	Weak transcription	Esophagus	oesophagus
13	chr1:75195400-75197800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:75195600-75198000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:75195600-75200400	Active TSS	A549	lung
16	chr1:75195800-75198000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:75195800-75198400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:75196000-75197800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr1:75196200-75198000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:75196400-75198000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:75196400-75198200	Weak transcription	HSMMtube	muscle
22	chr1:75196400-75198400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr1:75196400-75199600	Active TSS	Fetal Kidney	kidney
24	chr1:75196600-75198400	Active TSS	HepG2	liver
25	chr1:75196800-75197800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr1:75196800-75197800	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr1:75196800-75198000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr1:75196800-75198600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:75196800-75200000	Active TSS	Fetal Intestine Large	intestine
30	chr1:75197000-75197800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:75197000-75197800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:75197000-75197800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:75197000-75197800	Flanking Active TSS	Colon Smooth Muscle	Colon
34	chr1:75197000-75198000	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr1:75197000-75198200	Enhancers	Fetal Lung	lung
36	chr1:75197000-75198200	Flanking Active TSS	HUVEC	blood vessel
37	chr1:75197000-75199000	Active TSS	Stomach Smooth Muscle	stomach
38	chr1:75197000-75199600	Active TSS	Fetal Intestine Small	intestine
39	chr1:75197000-75199600	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr1:75197200-75197800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:75197200-75197800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:75197200-75197800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:75197200-75197800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr1:75197200-75197800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:75197200-75197800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:75197200-75197800	Enhancers	Brain Angular Gyrus	brain
47	chr1:75197200-75197800	Enhancers	Brain Anterior Caudate	brain
48	chr1:75197200-75197800	Flanking Active TSS	Fetal Stomach	stomach
49	chr1:75197200-75197800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr1:75197200-75197800	Flanking Active TSS	Rectal Smooth Muscle	rectum

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