Variant report

Variant	rs1013129
Chromosome Location	chr21:40498109-40498110
allele	A/G
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	CTCF	chr21:40498000-40498150	AoAF	blood vessel:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
2	RAD21	chr21:40497883-40498185	K562	blood:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
3	MAZ	chr21:40497936-40498127	K562	blood:	n/a	n/a
4	RAD21	chr21:40497635-40498259	H1-hESC	embryonic stem cell:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
5	CTCF	chr21:40498020-40498170	BJ	skin:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
6	RAD21	chr21:40497758-40498292	A549	lung:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
7	CTCF	chr21:40497980-40498130	GM12866	blood:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
8	MAX	chr21:40497861-40498143	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr21:40497980-40498130	SAEC	small airway:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
10	CTCF	chr21:40497940-40498214	K562	blood:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
11	CTCF	chr21:40498000-40498150	HCFaa	heart:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
12	RAD21	chr21:40497650-40498387	ECC-1	luminal epithelium:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
13	CTCF	chr21:40498000-40498150	GM12874	blood:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
14	SMC3	chr21:40497748-40498264	Hela-S3	cervix:	n/a	chr21:40498057-40498071
15	CTCF	chr21:40497935-40498193	GM19238	blood:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
16	CEBPB	chr21:40497807-40498325	MCF-7	breast:	n/a	chr21:40498084-40498095
17	CTCF	chr21:40498000-40498150	HA-sp	spinal cord:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
18	ZNF143	chr21:40497890-40498188	GM12878	blood:	n/a	n/a
19	MAFK	chr21:40497949-40498159	HepG2	liver:	n/a	n/a
20	CTCF	chr21:40497960-40498110	NHLF	lung:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
21	CTCF	chr21:40497942-40498177	Hela-S3	cervix:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
22	CTCF	chr21:40497943-40498185	HepG2	liver:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
23	CTCF	chr21:40497930-40498209	Kidney_OC	kidney:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
24	RAD21	chr21:40497802-40498367	HCT-116	colon:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
25	CTCF	chr21:40498000-40498150	HepG2	liver:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
26	CTCF	chr21:40497940-40498203	LNCaP	prostate:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
27	CEBPB	chr21:40497837-40498337	MCF-7	breast:	n/a	chr21:40498084-40498095
28	CTCF	chr21:40497980-40498130	HepG2	liver:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
29	CTCF	chr21:40498020-40498170	HCT-116	colon:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
30	CTCF	chr21:40497960-40498110	GM12874	blood:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
31	CEBPB	chr21:40497943-40498240	K562	blood:	n/a	chr21:40498084-40498095
32	CTCF	chr21:40497943-40498150	GM19239	blood:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
33	CTCF	chr21:40498000-40498150	AG04449	skin:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
34	RAD21	chr21:40497257-40498635	SK-N-SH	brain:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
35	CTCF	chr21:40498000-40498150	AG09319	gingival:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
36	CTCF	chr21:40497960-40498110	RPTEC	kidney:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
37	RCOR1	chr21:40497913-40498113	K562	blood:	n/a	n/a
38	RAD21	chr21:40497707-40498304	IMR90	lung:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
39	CTCF	chr21:40497888-40498193	SK-N-SH_RA	brain:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
40	RAD21	chr21:40497907-40498156	K562	blood:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
41	CTCF	chr21:40497980-40498130	RPTEC	kidney:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
42	CTCF	chr21:40497980-40498130	BJ	skin:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
43	ZNF143	chr21:40497882-40498235	H1-hESC	embryonic stem cell:	n/a	n/a
44	CTCF	chr21:40498000-40498150	GM12864	blood:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
45	MAX	chr21:40497456-40498317	MCF-7	breast:	n/a	n/a
46	CTCF	chr21:40497884-40498139	A549	lung:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
47	RAD21	chr21:40497588-40498327	H1-hESC	embryonic stem cell:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
48	CEBPB	chr21:40497897-40498264	A549	lung:	n/a	chr21:40498084-40498095
49	CTCF	chr21:40497980-40498130	GM12872	blood:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
50	RAD21	chr21:40497898-40498210	GM12878	blood:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126

No.	Distal block	Cell Line	Cell type
1	chr21:40105498..40106623-chr21:40497124..40499103,7	MCF-7	breast:
2	chr21:40480387..40482431-chr21:40496618..40498616,2	MCF-7	breast:
3	chr21:40460586..40461779-chr21:40497559..40498490,3	MCF-7	breast:
4	chr21:40493420..40495416-chr21:40496679..40498868,2	K562	blood:
5	chr21:40176646..40177691-chr21:40497667..40498470,3	MCF-7	breast:
6	chr21:40468353..40468958-chr21:40497933..40498489,3	MCF-7	breast:
7	chr21:40488161..40490338-chr21:40496446..40499117,2	K562	blood:
8	chr21:40496928..40499014-chr21:40502516..40504228,2	K562	blood:
9	chr21:40176334..40177511-chr21:40497580..40498463,5	MCF-7	breast:

Variant related genes	Relation type
RPL23AP12	TF binding region
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1810383	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1810384	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882777	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2142112	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297255	0.84[CHD][hapmap]
rs2836895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836936	0.84[CHD][hapmap]
rs2836941	0.84[CHD][hapmap]
rs2836979	0.84[CHD][hapmap]
rs373728	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs375073	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs420888	0.84[CHD][hapmap]
rs431284	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431704	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442916	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs454902	0.83[ASN][1000 genomes]
rs6517516	0.84[CHD][hapmap]
rs7281540	0.84[CHD][hapmap]
rs7283826	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs909181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9305669	0.84[CHD][hapmap]
rs941385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9979691	0.84[CHD][hapmap]
rs9981595	0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1013129	RCAN1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40496000-40498400	Enhancers	Dnd41	blood
2	chr21:40496200-40498200	Enhancers	Stomach Smooth Muscle	stomach
3	chr21:40496200-40498400	Enhancers	Fetal Muscle Leg	muscle
4	chr21:40496200-40498400	Enhancers	NHDF-Ad	bronchial
5	chr21:40496200-40498600	Enhancers	HepG2	liver
6	chr21:40496200-40498800	Enhancers	Fetal Stomach	stomach
7	chr21:40496400-40498400	Enhancers	Fetal Lung	lung
8	chr21:40496400-40498800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr21:40496800-40498400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr21:40497000-40498400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr21:40497000-40498800	Enhancers	Lung	lung
12	chr21:40497400-40498400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr21:40497400-40498600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr21:40497600-40498200	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr21:40497600-40498200	Enhancers	Hela-S3	cervix
16	chr21:40497600-40498400	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr21:40497600-40498400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr21:40497800-40498200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr21:40497800-40498200	Enhancers	Brain Hippocampus Middle	brain
20	chr21:40497800-40498200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr21:40497800-40498800	Enhancers	Fetal Muscle Trunk	muscle
22	chr21:40497800-40506200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr21:40498000-40499200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr21:40498000-40500200	Weak transcription	Right Atrium	heart
25	chr21:40498000-40503000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr21:40498000-40503000	Weak transcription	Esophagus	oesophagus
27	chr21:40498000-40503200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr21:40498000-40503200	Weak transcription	Psoas Muscle	Psoas

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