Variant report

Variant	rs28654603
Chromosome Location	chr1:75197283-75197284
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr1:75196852-75197584	SK-N-SH	brain:	n/a	n/a
2	SP1	chr1:75197041-75197636	A549	lung:	n/a	n/a
3	CUX1	chr1:75196910-75198287	GM12878	blood:	n/a	n/a
4	CHD2	chr1:75197213-75198218	GM12878	blood:	n/a	n/a
5	TBL1XR1	chr1:75196846-75197486	K562	blood:	n/a	n/a
6	CEBPD	chr1:75197032-75197501	K562	blood:	n/a	n/a
7	TCF12	chr1:75196978-75197686	A549	lung:	n/a	n/a
8	HEY1	chr1:75197075-75198245	HepG2	liver:	n/a	n/a
9	RELA	chr1:75196976-75199695	GM19193	blood:	n/a	n/a
10	ARID3A	chr1:75196807-75197673	HepG2	liver:	n/a	n/a
11	MYC	chr1:75197038-75197464	K562	blood:	n/a	chr1:75197136-75197145 chr1:75197135-75197144
12	RELA	chr1:75197065-75199714	GM15510	blood:	n/a	n/a
13	NR3C1	chr1:75197099-75197549	A549	lung:	n/a	chr1:75197333-75197347 chr1:75197101-75197127
14	GATA3	chr1:75196807-75197658	A549	lung:	n/a	chr1:75197228-75197244
15	JUN	chr1:75196967-75197597	HepG2	liver:	n/a	chr1:75197135-75197144 chr1:75197136-75197144 chr1:75197136-75197143
16	ARID3A	chr1:75196885-75197457	K562	blood:	n/a	n/a
17	POLR2A	chr1:75197076-75197727	HepG2	liver:	n/a	n/a
18	TBP	chr1:75196893-75197557	GM12878	blood:	n/a	n/a
19	ATF2	chr1:75196957-75197766	GM12878	blood:	n/a	n/a
20	RELA	chr1:75197077-75199725	GM12891	blood:	n/a	n/a
21	HEY1	chr1:75196948-75198153	HepG2	liver:	n/a	n/a
22	RELA	chr1:75196990-75199882	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:75197126-75197598	K562	blood:	n/a	n/a
24	MTA3	chr1:75197225-75199820	GM12878	blood:	n/a	n/a
25	RELA	chr1:75197016-75199699	GM19099	blood:	n/a	n/a
26	MAFK	chr1:75197124-75197572	HepG2	liver:	n/a	n/a
27	POLR2A	chr1:75196850-75200950	GM12878	blood:	n/a	n/a
28	RCOR1	chr1:75197022-75197552	K562	blood:	n/a	n/a
29	POLR2A	chr1:75196955-75199695	HepG2	liver:	n/a	n/a
30	GATA3	chr1:75196910-75197572	SK-N-SH	brain:	n/a	chr1:75197228-75197244
31	ZMIZ1	chr1:75197104-75197376	K562	blood:	n/a	n/a
32	POLR2A	chr1:75197152-75197427	K562	blood:	n/a	n/a
33	TEAD4	chr1:75196907-75197767	HepG2	liver:	n/a	n/a
34	POLR2A	chr1:75196987-75201662	GM12891	blood:	n/a	n/a
35	POLR2A	chr1:75197176-75197450	HepG2	liver:	n/a	n/a
36	POLR2A	chr1:75197017-75197718	HepG2	liver:	n/a	n/a
37	RELA	chr1:75197115-75200040	GM18505	blood:	n/a	n/a
38	NFIC	chr1:75196996-75197747	HepG2	liver:	n/a	n/a
39	CEBPB	chr1:75197224-75197716	HepG2	liver:	n/a	n/a
40	POLR2A	chr1:75197128-75198271	GM12891	blood:	n/a	n/a
41	TAF1	chr1:75197248-75197499	HepG2	liver:	n/a	n/a
42	NFIC	chr1:75197115-75197665	HepG2	liver:	n/a	n/a
43	GATA3	chr1:75196780-75197754	SK-N-SH	brain:	n/a	chr1:75197228-75197244
44	POLR2A	chr1:75197241-75197531	A549	lung:	n/a	n/a
45	MXI1	chr1:75197095-75197656	HepG2	liver:	n/a	n/a
46	MYBL2	chr1:75197049-75197691	HepG2	liver:	n/a	n/a
47	ZNF384	chr1:75196761-75197618	GM12878	blood:	n/a	n/a
48	FOXA1	chr1:75197252-75197763	HepG2	liver:	n/a	n/a
49	POLR2A	chr1:75197004-75197790	HepG2	liver:	n/a	n/a
50	NR3C1	chr1:75197143-75197600	A549	lung:	n/a	chr1:75197333-75197347

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:75195743..75197778-chr1:75197921..75199580,2	MCF-7	breast:
2	chr1:75197237..75200127-chr1:76254006..76255529,2	K562	blood:

Variant related genes	Relation type
TYW3	TF binding region
ENSG00000162623	Chromatin interaction
ENSG00000116791	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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.93[EUR][1000 genomes]
rs28602706	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28640981	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28683801	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28685856	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28695657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28767547	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28796389	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28796647	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.98[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];0.94[EUR][1000 genomes]
rs3845357	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3889133	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55895041	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790736	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790737	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61790739	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749690	0.92[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	nsv871152	chr1:75152186-75197533	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
5	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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs28654603	CRYZ	cis	Esophagus Mucosa	GTEx
rs28654603	CRYZ	cis	Adipose Subcutaneous	GTEx
rs28654603	CRYZ	cis	Whole Blood	GTEx
rs28654603	CRYZ	cis	Artery Aorta	GTEx
rs28654603	TYW3	cis	Muscle Skeletal	GTEx
rs28654603	CRYZ	cis	Skin Sun Exposed Lower leg	GTEx
rs28654603	CRYZ	Cis_1M	lymphoblastoid	RTeQTL
rs28654603	CRYZ	cis	lung	GTEx
rs28654603	CRYZ	cis	Nerve Tibial	GTEx
rs28654603	CRYZ	cis	Artery Tibial	GTEx
rs28654603	CRYZ	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 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	chr1:75189400-75197400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:75189600-75197400	Weak transcription	Brain Hippocampus Middle	brain
7	chr1:75192200-75197400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:75192200-75197600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:75192200-75197800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:75192200-75198000	Weak transcription	Gastric	stomach
11	chr1:75192400-75197400	Weak transcription	Spleen	Spleen
12	chr1:75192400-75198000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:75192400-75198000	Weak transcription	Fetal Thymus	thymus
14	chr1:75192600-75197600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:75192800-75197600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr1:75193200-75197400	Weak transcription	Primary B cells from cord blood	blood
17	chr1:75194600-75198200	Weak transcription	Small Intestine	intestine
18	chr1:75194800-75198000	Weak transcription	Brain Substantia Nigra	brain
19	chr1:75194800-75198200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:75195000-75198000	Weak transcription	Esophagus	oesophagus
21	chr1:75195400-75197800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:75195600-75197400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr1:75195600-75198000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:75195600-75200400	Active TSS	A549	lung
25	chr1:75195800-75198000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr1:75195800-75198400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:75196000-75197800	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr1:75196200-75198000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:75196400-75197400	Enhancers	Hela-S3	cervix
30	chr1:75196400-75198000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:75196400-75198200	Weak transcription	HSMMtube	muscle
32	chr1:75196400-75198400	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr1:75196400-75199600	Active TSS	Fetal Kidney	kidney
34	chr1:75196600-75197400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:75196600-75197400	Active TSS	Liver	Liver
36	chr1:75196600-75198400	Active TSS	HepG2	liver
37	chr1:75196800-75197600	Enhancers	HSMM	muscle
38	chr1:75196800-75197800	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr1:75196800-75197800	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr1:75196800-75198000	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr1:75196800-75198600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr1:75196800-75200000	Active TSS	Fetal Intestine Large	intestine
43	chr1:75197000-75197400	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr1:75197000-75197600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr1:75197000-75197800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:75197000-75197800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:75197000-75197800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:75197000-75197800	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr1:75197000-75198000	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr1:75197000-75198200	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links