Variant report

Variant	rs7510385
Chromosome Location	chr21:40497741-40497742
allele	C/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	CTCF	chr21:40497688-40497765	Gliobla	brain:	n/a	n/a
2	RAD21	chr21:40497635-40498259	H1-hESC	embryonic stem cell:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
3	POLR2A	chr21:40497656-40497805	A549	lung:	n/a	n/a
4	RAD21	chr21:40497650-40498387	ECC-1	luminal epithelium:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
5	CTCF	chr21:40497598-40497880	GM19239	blood:	n/a	n/a
6	RAD21	chr21:40497257-40498635	SK-N-SH	brain:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
7	RAD21	chr21:40497707-40498304	IMR90	lung:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
8	POLR2A	chr21:40497697-40497886	HepG2	liver:	n/a	n/a
9	MYC	chr21:40497596-40497860	MCF-7	breast:	n/a	n/a
10	MAX	chr21:40497456-40498317	MCF-7	breast:	n/a	n/a
11	RAD21	chr21:40497588-40498327	H1-hESC	embryonic stem cell:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
12	CTCF	chr21:40497634-40497814	MCF-7	breast:	n/a	n/a
13	MAX	chr21:40497627-40498096	H1-hESC	embryonic stem cell:	n/a	n/a
14	MYC	chr21:40497738-40498203	NB4	blood:	n/a	n/a
15	CTCF	chr21:40497678-40497813	MCF-7	breast:	n/a	n/a
16	KAP1	chr21:40497638-40498142	HEK293	kidney:	n/a	n/a
17	CTCF	chr21:40497726-40498305	A549	lung:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
18	ESR1	chr21:40497731-40498107	ECC-1	luminal epithelium:	n/a	chr21:40497993-40498010 chr21:40497994-40498009
19	CTCF	chr21:40497622-40498606	SK-N-SH	brain:	n/a	chr21:40498056-40498072 chr21:40498055-40498073 chr21:40498050-40498071
20	CTCF	chr21:40497683-40497760	ProgFib	skin:	n/a	n/a
21	SMC3	chr21:40497671-40498342	HepG2	liver:	n/a	chr21:40498057-40498071
22	RAD21	chr21:40497694-40498316	SK-N-SH_RA	brain:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
23	RAD21	chr21:40497656-40498437	MCF-7	breast:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
24	MYC	chr21:40497666-40497780	MCF-7	breast:	n/a	n/a
25	RAD21	chr21:40497644-40498264	HepG2	liver:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
26	MAX	chr21:40497585-40498203	NB4	blood:	n/a	n/a
27	POLR2A	chr21:40497628-40497793	Gliobla	brain:	n/a	n/a
28	TCF12	chr21:40497737-40498176	H1-hESC	embryonic stem cell:	n/a	chr21:40497971-40497978
29	SIN3A	chr21:40497720-40498181	H1-hESC	embryonic stem cell:	n/a	n/a
30	EGR1	chr21:40497483-40497838	K562	blood:	n/a	n/a
31	CTCF	chr21:40497716-40497759	MCF-7	breast:	n/a	n/a
32	ESR1	chr21:40497715-40498135	ECC-1	luminal epithelium:	n/a	chr21:40497993-40498010 chr21:40497994-40498009
33	MYC	chr21:40497572-40497994	MCF-7	breast:	n/a	n/a
34	SMC3	chr21:40497459-40498802	SK-N-SH	brain:	n/a	chr21:40498057-40498071
35	CTCF	chr21:40497680-40497830	GM12875	blood:	n/a	n/a
36	CTCF	chr21:40497629-40497803	NHEK	skin:	n/a	n/a
37	RAD21	chr21:40497671-40498382	HCT-116	colon:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
38	EGR1	chr21:40497550-40497808	K562	blood:	n/a	n/a
39	RAD21	chr21:40497735-40498384	MCF-7	breast:	n/a	chr21:40497963-40497976 chr21:40498053-40498072 chr21:40498112-40498126
40	RAD21	chr21:40497686-40498292	H1-hESC	embryonic stem cell:	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	chr21:40495398..40498019-chr21:40544324..40546654,2	K562	blood:
5	chr21:40493420..40495416-chr21:40496679..40498868,2	K562	blood:
6	chr21:40176932..40179361-chr21:40495597..40497932,3	MCF-7	breast:
7	chr21:40176646..40177691-chr21:40497667..40498470,3	MCF-7	breast:
8	chr21:40488161..40490338-chr21:40496446..40499117,2	K562	blood:
9	chr21:40496928..40499014-chr21:40502516..40504228,2	K562	blood:
10	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: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11702077	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11702158	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242947	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2242948	0.83[ASN][1000 genomes]
rs2836894	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836896	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836897	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836898	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836899	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836900	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836903	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836904	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836905	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836906	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836908	0.84[ASN][1000 genomes]
rs2836909	0.82[ASN][1000 genomes]
rs2836911	0.82[ASN][1000 genomes]
rs34912726	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34989336	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4817990	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs56147949	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62224879	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8131292	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8131570	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40486600-40497800	Weak transcription	Thymus	Thymus
2	chr21:40496000-40498400	Enhancers	Dnd41	blood
3	chr21:40496200-40498000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr21:40496200-40498000	Enhancers	Fetal Heart	heart
5	chr21:40496200-40498200	Enhancers	Stomach Smooth Muscle	stomach
6	chr21:40496200-40498400	Enhancers	Fetal Muscle Leg	muscle
7	chr21:40496200-40498400	Enhancers	NHDF-Ad	bronchial
8	chr21:40496200-40498600	Enhancers	HepG2	liver
9	chr21:40496200-40498800	Enhancers	Fetal Stomach	stomach
10	chr21:40496400-40498000	Enhancers	Colon Smooth Muscle	Colon
11	chr21:40496400-40498000	Enhancers	Left Ventricle	heart
12	chr21:40496400-40498400	Enhancers	Fetal Lung	lung
13	chr21:40496400-40498800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr21:40496600-40497800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr21:40496600-40498000	Enhancers	Right Ventricle	heart
16	chr21:40496800-40498000	Enhancers	Liver	Liver
17	chr21:40496800-40498400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr21:40497000-40497800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr21:40497000-40497800	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr21:40497000-40498000	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr21:40497000-40498000	Enhancers	Duodenum Mucosa	Duodenum
22	chr21:40497000-40498000	Enhancers	Right Atrium	heart
23	chr21:40497000-40498400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr21:40497000-40498800	Enhancers	Lung	lung
25	chr21:40497400-40498000	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr21:40497400-40498000	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr21:40497400-40498000	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr21:40497400-40498000	Enhancers	NHLF	lung
29	chr21:40497400-40498400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr21:40497400-40498600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr21:40497600-40497800	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
32	chr21:40497600-40497800	Enhancers	Fetal Kidney	kidney
33	chr21:40497600-40497800	Flanking Active TSS	Rectal Smooth Muscle	rectum
34	chr21:40497600-40498000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr21:40497600-40498000	Enhancers	H1 Cell Line	embryonic stem cell
36	chr21:40497600-40498000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr21:40497600-40498000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr21:40497600-40498000	Enhancers	H9 Cell Line	embryonic stem cell
39	chr21:40497600-40498000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr21:40497600-40498000	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr21:40497600-40498000	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr21:40497600-40498000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr21:40497600-40498000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr21:40497600-40498000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr21:40497600-40498000	Enhancers	Primary hematopoietic stem cells	blood
46	chr21:40497600-40498000	Enhancers	Adipose Nuclei	Adipose
47	chr21:40497600-40498000	Enhancers	Brain Angular Gyrus	brain
48	chr21:40497600-40498000	Enhancers	Colonic Mucosa	Colon
49	chr21:40497600-40498000	Enhancers	Esophagus	oesophagus
50	chr21:40497600-40498000	Enhancers	Fetal Intestine Small	intestine

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