Variant report

Variant	rs12083211
Chromosome Location	chr1:153032131-153032132
allele	A/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	EGR1	chr1:153031877-153032149	K562	blood:	n/a	n/a
2	NR2F2	chr1:153031734-153032229	K562	blood:	n/a	n/a
3	EP300	chr1:153031681-153032143	K562	blood:	n/a	n/a
4	MAFK	chr1:153031687-153032192	K562	blood:	n/a	n/a
5	ATF1	chr1:153031406-153032192	K562	blood:	n/a	n/a
6	CBX3	chr1:153031761-153032266	K562	blood:	n/a	n/a
7	RCOR1	chr1:153031363-153032281	K562	blood:	n/a	n/a
8	IRF1	chr1:153031804-153032273	K562	blood:	n/a	n/a
9	JUN	chr1:153031244-153032433	K562	blood:	n/a	chr1:153031936-153031944 chr1:153031932-153031943
10	MAX	chr1:153031763-153032306	K562	blood:	n/a	n/a
11	MYC	chr1:153031411-153032218	K562	blood:	n/a	n/a
12	JUND	chr1:153031299-153032286	K562	blood:	n/a	chr1:153031936-153031944 chr1:153031932-153031943
13	TAL1	chr1:153031329-153032288	K562	blood:	n/a	chr1:153031988-153032006
14	NR2F2	chr1:153031647-153032316	K562	blood:	n/a	n/a
15	MAZ	chr1:153031838-153032268	K562	blood:	n/a	n/a
16	GABPA	chr1:153031811-153032182	K562	blood:	n/a	n/a
17	FOS	chr1:153031747-153032180	K562	blood:	n/a	chr1:153031934-153031945 chr1:153031936-153031944 chr1:153031932-153031943
18	POLR2A	chr1:153032102-153032238	K562	blood:	n/a	n/a
19	GATA3	chr1:153031620-153032147	SK-N-SH	brain:	n/a	chr1:153031989-153032006 chr1:153031937-153031946 chr1:153031934-153031943
20	PML	chr1:153031487-153032259	K562	blood:	n/a	n/a
21	TEAD4	chr1:153031212-153032404	K562	blood:	n/a	n/a
22	GABPA	chr1:153031842-153032223	K562	blood:	n/a	n/a
23	CCNT2	chr1:153031399-153032490	K562	blood:	n/a	chr1:153031986-153032006
24	HDAC2	chr1:153031785-153032169	K562	blood:	n/a	n/a
25	CEBPB	chr1:153031752-153032198	K562	blood:	n/a	n/a
26	GATA2	chr1:153031269-153032177	HUVEC	blood vessel:	n/a	chr1:153031478-153031485 chr1:153031471-153031492 chr1:153031425-153031435 chr1:153031424-153031436 chr1:153031983-153031997 chr1:153031478-153031485 chr1:153031473-153031489 chr1:153031473-153031489 chr1:153031989-153032006 chr1:153031426-153031433 chr1:153031937-153031946 chr1:153031934-153031943 chr1:153031478-153031485 chr1:153031426-153031435
27	ZNF143	chr1:153031955-153032131	K562	blood:	n/a	n/a
28	CEBPD	chr1:153031328-153032328	K562	blood:	n/a	n/a
29	TRIM28	chr1:153031649-153032270	K562	blood:	n/a	n/a
30	JUN	chr1:153031440-153032196	K562	blood:	n/a	chr1:153031936-153031944 chr1:153031932-153031943
31	TBL1XR1	chr1:153031314-153032255	K562	blood:	n/a	n/a
32	UBTF	chr1:153031907-153032233	K562	blood:	n/a	n/a
33	GATA1	chr1:153030928-153032560	K562	blood:	n/a	chr1:153031478-153031485 chr1:153031471-153031492 chr1:153031425-153031435 chr1:153031424-153031436 chr1:153031478-153031485 chr1:153031473-153031489 chr1:153031473-153031489 chr1:153032399-153032409 chr1:153031989-153032006 chr1:153031426-153031433 chr1:153031937-153031946 chr1:153031934-153031943 chr1:153031478-153031485 chr1:153031426-153031435
34	HCFC1	chr1:153031932-153032132	K562	blood:	n/a	n/a
35	BHLHE40	chr1:153031557-153032209	K562	blood:	n/a	n/a
36	POLR2A	chr1:153031752-153032197	K562	blood:	n/a	n/a
37	PML	chr1:153031717-153032273	K562	blood:	n/a	n/a
38	EGR1	chr1:153031790-153032246	K562	blood:	n/a	n/a
39	HMGN3	chr1:153031774-153032184	K562	blood:	n/a	n/a
40	TEAD4	chr1:153031309-153032323	K562	blood:	n/a	n/a
41	POLR2A	chr1:153031870-153032192	K562	blood:	n/a	n/a
42	YY1	chr1:153031862-153032171	K562	blood:	n/a	n/a
43	JUN	chr1:153031765-153032183	K562	blood:	n/a	chr1:153031936-153031944 chr1:153031932-153031943
44	GATA2	chr1:153031564-153032230	K562	blood:	n/a	chr1:153031983-153031997 chr1:153031989-153032006 chr1:153031937-153031946 chr1:153031934-153031943
45	GATA1	chr1:153031734-153032190	K562	blood:	n/a	chr1:153031989-153032006 chr1:153031937-153031946 chr1:153031934-153031943
46	GATA1	chr1:153031769-153032211	PBDEFetal	blood:	n/a	chr1:153031989-153032006 chr1:153031937-153031946 chr1:153031934-153031943
47	MAX	chr1:153031496-153032270	K562	blood:	n/a	n/a
48	REST	chr1:153031832-153032170	K562	blood:	n/a	n/a
49	EP300	chr1:153031276-153032385	K562	blood:	n/a	chr1:153031340-153031354 chr1:153031495-153031509
50	GATA1	chr1:153031315-153032513	PBDE	blood:	n/a	chr1:153031478-153031485 chr1:153031471-153031492 chr1:153031425-153031435 chr1:153031424-153031436 chr1:153031478-153031485 chr1:153031473-153031489 chr1:153031473-153031489 chr1:153032399-153032409 chr1:153031989-153032006 chr1:153031426-153031433 chr1:153031937-153031946 chr1:153031934-153031943 chr1:153031478-153031485 chr1:153031426-153031435

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153031331..153032975-chr1:153077540..153080303,2	K562	blood:

Variant related genes	Relation type
SPRR2A	TF binding region
ENSG00000203785	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10888524	0.83[TSI][hapmap]
rs10888528	0.91[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10888529	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1108410	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11205174	0.83[TSI][hapmap]
rs11205175	0.83[TSI][hapmap]
rs11205179	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11205180	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11205181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11205182	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11205185	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11205186	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11205187	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11205188	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11205189	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11485498	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11488175	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11576797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11587269	0.84[CEU][hapmap]
rs11590835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11812015	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12079087	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12082627	0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12734348	0.88[CHB][hapmap]
rs1334849	0.83[TSI][hapmap]
rs1415965	0.83[TSI][hapmap]
rs1415966	0.83[TSI][hapmap]
rs1415972	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs1500937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1577960	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1933382	0.83[TSI][hapmap]
rs1995308	0.88[CEU][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs28924721	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs310109	0.83[TSI][hapmap]
rs310126	0.83[TSI][hapmap]
rs3181787	0.83[TSI][hapmap]
rs3737864	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409986	0.83[TSI][hapmap]
rs440598	0.83[TSI][hapmap]
rs441229	0.81[TSI][hapmap]
rs454245	0.85[TSI][hapmap]
rs4845513	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs4845519	0.83[TSI][hapmap]
rs55906223	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56158137	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56412380	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs576941	0.83[TSI][hapmap]
rs582345	0.83[TSI][hapmap]
rs61811886	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61811902	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61811903	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6587725	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs662506	0.83[TSI][hapmap]
rs6660797	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6660878	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6661059	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6661063	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6664380	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670380	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6673356	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6675009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6677674	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6680061	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6683514	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6686526	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689066	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6689510	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6692062	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6693927	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6698361	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7531076	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7532166	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7540609	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7543689	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7548977	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7551791	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv1003756	chr1:152944201-153044621	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	esv3424702	chr1:153015726-153032343	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12083211	S100A7A	cis	parietal	SCAN
rs12083211	SPRR1B	cis	parietal	SCAN
rs12083211	ATP8B2	cis	parietal	SCAN
rs12083211	PGLYRP4	cis	parietal	SCAN
rs12083211	BNIPL	cis	cerebellum	SCAN
rs12083211	LCE2B	cis	parietal	SCAN
rs12083211	SPRR1B	cis	Skin Sun Exposed Lower leg	GTEx
rs12083211	THEM5	cis	cerebellum	SCAN
rs12083211	RAB13	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153029800-153032400	Enhancers	NHEK	skin
2	chr1:153030000-153032400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:153030800-153032200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:153031400-153032200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:153031400-153032200	Enhancers	HMEC	breast
6	chr1:153031600-153032200	Enhancers	Placenta	Placenta
7	chr1:153031600-153032200	Enhancers	Pancreas	Pancrea
8	chr1:153031600-153032200	Enhancers	Placenta Amnion	Placenta Amnion
9	chr1:153031600-153032400	Flanking Active TSS	K562	blood
10	chr1:153031800-153032200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:153031800-153032400	Enhancers	Gastric	stomach
12	chr1:153032000-153032200	Enhancers	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links