Variant report

Variant	rs28640981
Chromosome Location	chr1:75199484-75199485
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:327)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:327 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:75199480-75199630	HPF	lung:	n/a	n/a
2	CUX1	chr1:75198508-75199670	K562	blood:	n/a	n/a
3	RAD21	chr1:75199354-75199738	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:75199329-75199620	GM12891	blood:	n/a	n/a
5	MYC	chr1:75198487-75199709	MCF10A-Er-Src	breast:	n/a	n/a
6	CTCF	chr1:75199460-75199610	GM12866	blood:	n/a	n/a
7	CTCF	chr1:75199480-75199630	HFF-Myc	foreskin:	n/a	n/a
8	POLR2A	chr1:75198636-75200123	IMR90	lung:	n/a	n/a
9	RELA	chr1:75196976-75199695	GM19193	blood:	n/a	n/a
10	CTCF	chr1:75199444-75199722	Medullo	brain:	n/a	n/a
11	FOS	chr1:75199409-75200096	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr1:75198629-75199853	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr1:75199459-75199702	LNCaP	prostate:	n/a	n/a
14	HCFC1	chr1:75198603-75199689	K562	blood:	n/a	n/a
15	MXI1	chr1:75198396-75199698	HepG2	liver:	n/a	n/a
16	CTCF	chr1:75199480-75199630	HEK293	kidney:	n/a	n/a
17	CTCF	chr1:75199480-75199630	BE2_C	brain:	n/a	n/a
18	TBP	chr1:75198394-75199677	H1-hESC	embryonic stem cell:	n/a	n/a
19	RELA	chr1:75197065-75199714	GM15510	blood:	n/a	n/a
20	ATF1	chr1:75199418-75199743	K562	blood:	n/a	n/a
21	CTCF	chr1:75199460-75199610	HCFaa	heart:	n/a	n/a
22	KAP1	chr1:75199458-75199669	K562	blood:	n/a	n/a
23	POLR2A	chr1:75198271-75199697	K562	blood:	n/a	n/a
24	MAZ	chr1:75198620-75199645	HepG2	liver:	n/a	n/a
25	POLR2A	chr1:75199349-75199609	Hela-S3	cervix:	n/a	n/a
26	MXI1	chr1:75198512-75199712	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:75199371-75199662	GM12891	blood:	n/a	n/a
28	STAT3	chr1:75199313-75199591	MCF10A-Er-Src	breast:	n/a	n/a
29	CTCF	chr1:75199358-75199742	K562	blood:	n/a	n/a
30	CTCF	chr1:75199460-75199610	HBMEC	blood vessel:	n/a	n/a
31	CTCF	chr1:75199460-75199610	HAc	cerebellar:	n/a	n/a
32	CTCF	chr1:75199480-75199630	RPTEC	kidney:	n/a	n/a
33	CTCF	chr1:75199459-75199664	HepG2	liver:	n/a	n/a
34	POLR2A	chr1:75198510-75199668	Hela-S3	cervix:	n/a	n/a
35	BACH1	chr1:75199266-75200027	K562	blood:	n/a	n/a
36	POLR2A	chr1:75198317-75199727	GM12892	blood:	n/a	n/a
37	CTCF	chr1:75199431-75199696	Hela-S3	cervix:	n/a	n/a
38	FOXM1	chr1:75198400-75199698	GM12878	blood:	n/a	n/a
39	YY1	chr1:75198507-75199675	SK-N-SH_RA	brain:	n/a	chr1:75198846-75198868
40	POLR2A	chr1:75198430-75199823	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr1:75198304-75199550	HepG2	liver:	n/a	n/a
42	CTCF	chr1:75199416-75199623	T-47D	breast:	n/a	n/a
43	CTCF	chr1:75199456-75199665	MCF-7	breast:	n/a	n/a
44	CTCF	chr1:75199453-75199683	Pancreas_OC	pancreas:	n/a	n/a
45	RCOR1	chr1:75198071-75199802	GM12878	blood:	n/a	n/a
46	CTCF	chr1:75199460-75199610	GM12875	blood:	n/a	n/a
47	MAX	chr1:75198301-75199808	HepG2	liver:	n/a	n/a
48	CTCF	chr1:75199425-75199658	SK-N-SH_RA	brain:	n/a	n/a
49	CTCF	chr1:75199480-75199630	HMF	breast:	n/a	n/a
50	RELA	chr1:75197077-75199725	GM12891	blood:	n/a	n/a

No data

(count:7 , 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:
7	chr1:75198658..75199512-chr3:172428576..172429251,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
TYW3	TF binding region
CRYZ	TF binding region
ENSG00000201487	Chromatin interaction
ENSG00000162621	Chromatin interaction
ENSG00000144959	Chromatin interaction
ENSG00000162623	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10161	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12125889	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12129513	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1424671	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1574941	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1590639	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17618340	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2345438	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535522	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28588069	0.81[AMR][1000 genomes]
rs28594379	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28602706	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654603	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28683801	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28685856	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695657	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28767547	0.83[AMR][1000 genomes]
rs28796389	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28796647	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28804435	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831813	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35497701	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845356	0.81[AMR][1000 genomes]
rs3845357	0.81[AMR][1000 genomes]
rs3889133	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55895041	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790736	1.00[ASN][1000 genomes]
rs61790737	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61790739	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6668736	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs749690	0.83[AMR][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28640981	CRYZ	cis	Esophagus Mucosa	GTEx
rs28640981	CRYZ	cis	multi-tissue	Pritchard
rs28640981	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs28640981	CRYZ	cis	lung	GTEx
rs28640981	CRYZ	cis	Nerve Tibial	GTEx
rs28640981	CRYZ	cis	Adipose Subcutaneous	GTEx
rs28640981	CRYZ	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75195600-75200400	Active TSS	A549	lung
2	chr1:75196400-75199600	Active TSS	Fetal Kidney	kidney
3	chr1:75196800-75200000	Active TSS	Fetal Intestine Large	intestine
4	chr1:75197000-75199600	Active TSS	Fetal Intestine Small	intestine
5	chr1:75197000-75199600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr1:75197200-75199600	Active TSS	Pancreas	Pancrea
7	chr1:75197200-75199800	Active TSS	Colonic Mucosa	Colon
8	chr1:75197200-75200000	Active TSS	Right Atrium	heart
9	chr1:75197200-75200400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:75197400-75200000	Active TSS	Osteobl	bone
11	chr1:75197600-75199600	Active TSS	Left Ventricle	heart
12	chr1:75197600-75199600	Active TSS	Rectal Mucosa Donor 31	rectum
13	chr1:75197600-75199800	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr1:75197600-75199800	Active TSS	Aorta	Aorta
15	chr1:75197600-75200000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:75197600-75200000	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr1:75197600-75200000	Active TSS	Muscle Satellite Cultured Cells	--
18	chr1:75197600-75200000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:75197600-75200200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:75197600-75200200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:75197600-75200200	Active TSS	Ovary	ovary
22	chr1:75197600-75200400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:75197600-75200600	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr1:75197800-75199600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:75197800-75199600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr1:75197800-75199600	Active TSS	Liver	Liver
27	chr1:75197800-75199600	Active TSS	Colon Smooth Muscle	Colon
28	chr1:75197800-75199600	Active TSS	Duodenum Mucosa	Duodenum
29	chr1:75197800-75199600	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr1:75197800-75199600	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr1:75197800-75199600	Active TSS	Rectal Smooth Muscle	rectum
32	chr1:75197800-75199800	Active TSS	NHEK	skin
33	chr1:75197800-75200000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:75197800-75200000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:75197800-75200200	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr1:75197800-75200200	Active TSS	NHDF-Ad	bronchial
37	chr1:75197800-75200800	Active TSS	NHLF	lung
38	chr1:75197800-75201800	Active TSS	GM12878-XiMat	blood
39	chr1:75198000-75199600	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr1:75198000-75199600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:75198000-75199600	Active TSS	Brain Angular Gyrus	brain
42	chr1:75198000-75199600	Active TSS	Brain Anterior Caudate	brain
43	chr1:75198000-75199600	Active TSS	Gastric	stomach
44	chr1:75198000-75199600	Active TSS	Placenta Amnion	Placenta Amnion
45	chr1:75198000-75199800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:75198000-75199800	Active TSS	Brain Hippocampus Middle	brain
47	chr1:75198000-75199800	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr1:75198000-75199800	Active TSS	Brain Substantia Nigra	brain
49	chr1:75198000-75199800	Active TSS	Fetal Brain Female	brain
50	chr1:75198000-75199800	Active TSS	HSMM	muscle

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