Variant report

Variant	rs3889133
Chromosome Location	chr1:75198345-75198346
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:78)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:78 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr1:75196976-75199695	GM19193	blood:	n/a	n/a
2	POU2F2	chr1:75198309-75199248	GM12878	blood:	n/a	n/a
3	RELA	chr1:75197065-75199714	GM15510	blood:	n/a	n/a
4	POLR2A	chr1:75198271-75199697	K562	blood:	n/a	n/a
5	YY1	chr1:75198308-75199357	GM12878	blood:	n/a	chr1:75198846-75198868
6	POLR2A	chr1:75198280-75199302	GM12892	blood:	n/a	n/a
7	POLR2A	chr1:75198317-75199727	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:75198304-75199550	HepG2	liver:	n/a	n/a
9	RCOR1	chr1:75198071-75199802	GM12878	blood:	n/a	n/a
10	MAX	chr1:75198301-75199808	HepG2	liver:	n/a	n/a
11	RELA	chr1:75197077-75199725	GM12891	blood:	n/a	n/a
12	WRNIP1	chr1:75198316-75199620	GM12878	blood:	n/a	n/a
13	CTCF	chr1:75198300-75198450	HepG2	liver:	n/a	n/a
14	RELA	chr1:75196990-75199882	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:75198345-75199714	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr1:75198155-75199687	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:75198298-75198595	GM12878	blood:	n/a	n/a
18	SIN3A	chr1:75198056-75199697	H1-hESC	embryonic stem cell:	n/a	n/a
19	MTA3	chr1:75197225-75199820	GM12878	blood:	n/a	n/a
20	BCLAF1	chr1:75198313-75199218	GM12878	blood:	n/a	n/a
21	RELA	chr1:75197016-75199699	GM19099	blood:	n/a	n/a
22	POLR2A	chr1:75196850-75200950	GM12878	blood:	n/a	n/a
23	MTA3	chr1:75198303-75199793	GM12878	blood:	n/a	n/a
24	EBF1	chr1:75197606-75198573	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:75197951-75199663	GM12892	blood:	n/a	n/a
26	POLR2A	chr1:75196955-75199695	HepG2	liver:	n/a	n/a
27	POLR2A	chr1:75196987-75201662	GM12891	blood:	n/a	n/a
28	RELA	chr1:75197115-75200040	GM18505	blood:	n/a	n/a
29	TAF1	chr1:75198292-75199379	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr1:75198287-75198406	A549	lung:	n/a	n/a
31	POLR2A	chr1:75198268-75199689	NB4	blood:	n/a	n/a
32	POLR2A	chr1:75198331-75199842	K562	blood:	n/a	n/a
33	POLR2A	chr1:75198066-75199661	GM18526	blood:	n/a	n/a
34	MAZ	chr1:75197982-75199768	GM12878	blood:	n/a	n/a
35	PAX5	chr1:75197505-75199249	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:75198321-75199270	GM12891	blood:	n/a	n/a
37	POLR2A	chr1:75198302-75199421	U87	brain:	n/a	n/a
38	POLR2A	chr1:75198022-75199646	HepG2	liver:	n/a	n/a
39	RELA	chr1:75196917-75199189	GM18526	blood:	n/a	n/a
40	POLR2A	chr1:75198298-75199324	GM12891	blood:	n/a	n/a
41	POLR2A	chr1:75198314-75199258	HepG2	liver:	n/a	n/a
42	CEBPB	chr1:75197458-75199569	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:75198308-75199601	U87	brain:	n/a	n/a
44	RUNX3	chr1:75197477-75198369	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:75198295-75199733	HUVEC	blood vessel:	n/a	n/a
46	EP300	chr1:75197991-75199685	GM12878	blood:	n/a	chr1:75198210-75198226 chr1:75198820-75198829
47	MAX	chr1:75198294-75199832	A549	lung:	n/a	n/a
48	POLR2A	chr1:75197788-75199678	GM15510	blood:	n/a	n/a
49	MAZ	chr1:75198335-75199711	K562	blood:	n/a	n/a
50	HCFC1	chr1:75198319-75199757	Hela-S3	cervix:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:75197640..75200637-chr1:75200867..75204722,5	MCF-7	breast:
2	chr1:75198241..75199185-chr6:89791480..89792312,2	Hela-S3	cervix:
3	chr1:75197237..75200127-chr1:76254006..76255529,2	K562	blood:
4	chr1:75197578..75200968-chr1:75201632..75206969,6	MCF-7	breast:

No data

Variant related genes	Relation type
TYW3	TF binding region
ENSG00000146278	Chromatin interaction
ENSG00000162623	Chromatin interaction
ENSG00000201487	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10161	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12125889	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12129513	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1424671	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1574941	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1590639	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17618340	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2345438	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535522	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28594379	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28602706	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28640981	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654603	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28683801	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28685856	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695657	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28767547	0.82[AMR][1000 genomes]
rs28796389	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28796647	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28804435	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28831813	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35497701	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55895041	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790736	1.00[ASN][1000 genomes]
rs61790737	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61790739	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6668736	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs749690	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	esv10394	chr1:75198172-75198656	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3889133	CRYZ	cis	multi-tissue	Pritchard
rs3889133	CRYZ	cis	Nerve Tibial	GTEx
rs3889133	CRYZ	cis	Adipose Subcutaneous	GTEx
rs3889133	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs3889133	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs3889133	CRYZ	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75183000-75198400	Weak transcription	Fetal Brain Male	brain
2	chr1:75195600-75200400	Active TSS	A549	lung
3	chr1:75195800-75198400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:75196400-75198400	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr1:75196400-75199600	Active TSS	Fetal Kidney	kidney
6	chr1:75196600-75198400	Active TSS	HepG2	liver
7	chr1:75196800-75198600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:75196800-75200000	Active TSS	Fetal Intestine Large	intestine
9	chr1:75197000-75199000	Active TSS	Stomach Smooth Muscle	stomach
10	chr1:75197000-75199600	Active TSS	Fetal Intestine Small	intestine
11	chr1:75197000-75199600	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr1:75197200-75198400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:75197200-75198400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:75197200-75198400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:75197200-75199600	Active TSS	Pancreas	Pancrea
16	chr1:75197200-75199800	Active TSS	Colonic Mucosa	Colon
17	chr1:75197200-75200000	Active TSS	Right Atrium	heart
18	chr1:75197200-75200400	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr1:75197400-75198400	Enhancers	Spleen	Spleen
20	chr1:75197400-75200000	Active TSS	Osteobl	bone
21	chr1:75197600-75199600	Active TSS	Left Ventricle	heart
22	chr1:75197600-75199600	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr1:75197600-75199800	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr1:75197600-75199800	Active TSS	Aorta	Aorta
25	chr1:75197600-75200000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:75197600-75200000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr1:75197600-75200000	Active TSS	Muscle Satellite Cultured Cells	--
28	chr1:75197600-75200000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:75197600-75200200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:75197600-75200200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:75197600-75200200	Active TSS	Ovary	ovary
32	chr1:75197600-75200400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:75197600-75200600	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr1:75197800-75198400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:75197800-75198400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:75197800-75198400	Weak transcription	Fetal Heart	heart
37	chr1:75197800-75198800	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr1:75197800-75199600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:75197800-75199600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr1:75197800-75199600	Active TSS	Liver	Liver
41	chr1:75197800-75199600	Active TSS	Colon Smooth Muscle	Colon
42	chr1:75197800-75199600	Active TSS	Duodenum Mucosa	Duodenum
43	chr1:75197800-75199600	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr1:75197800-75199600	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr1:75197800-75199600	Active TSS	Rectal Smooth Muscle	rectum
46	chr1:75197800-75199800	Active TSS	NHEK	skin
47	chr1:75197800-75200000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:75197800-75200000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:75197800-75200200	Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr1:75197800-75200200	Active TSS	NHDF-Ad	bronchial

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