Variant report

Variant	rs7277627
Chromosome Location	chr21:40813558-40813559
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	ZNF384	chr21:40813455-40813782	K562	blood:	n/a	n/a
2	CTCF	chr21:40813521-40813731	Kidney_OC	kidney:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
3	CTCF	chr21:40813515-40813740	NHEK	skin:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
4	YY1	chr21:40813533-40813674	GM12878	blood:	n/a	n/a
5	CTCF	chr21:40813520-40813670	HMEC	breast:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
6	RAD21	chr21:40813438-40813785	K562	blood:	n/a	chr21:40813613-40813632
7	CTCF	chr21:40813520-40813670	NHDF-neo	bronchial:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
8	SMC3	chr21:40813447-40813809	GM12878	blood:	n/a	n/a
9	CTCF	chr21:40813540-40813690	HepG2	liver:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
10	CTCF	chr21:40813310-40813792	HCT-116	colon:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
11	RAD21	chr21:40813420-40813814	H1-hESC	embryonic stem cell:	n/a	chr21:40813613-40813632
12	CTCF	chr21:40813524-40813716	GM19240	blood:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
13	CTCF	chr21:40813515-40813727	HepG2	liver:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
14	CTCF	chr21:40813540-40813690	SAEC	small airway:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
15	CTCF	chr21:40813540-40813690	AG09319	gingival:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
16	CTCF	chr21:40813456-40813710	SK-N-SH_RA	brain:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
17	RAD21	chr21:40813456-40813724	K562	blood:	n/a	chr21:40813613-40813632
18	UBTF	chr21:40813415-40813766	K562	blood:	n/a	n/a
19	CTCF	chr21:40813373-40813845	MCF-7	breast:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
20	CTCF	chr21:40813540-40813690	HPF	lung:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
21	CTCF	chr21:40813540-40813690	K562	blood:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
22	CTCF	chr21:40813500-40813650	HCT-116	colon:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
23	CTCF	chr21:40813513-40813744	GM10266	blood:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
24	CTCF	chr21:40813540-40813690	BJ	skin:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
25	CTCF	chr21:40813495-40813791	Medullo	brain:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
26	CTCF	chr21:40813476-40813717	HepG2	liver:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
27	CTCF	chr21:40813459-40813752	K562	blood:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
28	BHLHE40	chr21:40813323-40813753	K562	blood:	n/a	n/a
29	RAD21	chr21:40813286-40813884	MCF-7	breast:	n/a	chr21:40813613-40813632
30	CTCF	chr21:40813530-40813689	SK-N-SH_RA	brain:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
31	MAZ	chr21:40813449-40813781	K562	blood:	n/a	n/a
32	RAD21	chr21:40813414-40813878	A549	lung:	n/a	chr21:40813613-40813632
33	CTCF	chr21:40813540-40813690	HUVEC	blood vessel:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
34	JUND	chr21:40813468-40813783	K562	blood:	n/a	n/a
35	RAD21	chr21:40813343-40813697	K562	blood:	n/a	chr21:40813613-40813632
36	MAFK	chr21:40813357-40813770	K562	blood:	n/a	n/a
37	CTCF	chr21:40813520-40813670	HFF	foreskin:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
38	RCOR1	chr21:40813481-40813766	K562	blood:	n/a	n/a
39	CTCF	chr21:40813430-40813833	H1-hESC	embryonic stem cell:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
40	CTCF	chr21:40813503-40813764	Hela-S3	cervix:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
41	CTCF	chr21:40813540-40813690	HRPEpiC	eye:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
42	CTCF	chr21:40813540-40813690	GM12871	blood:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
43	CTCF	chr21:40813509-40813756	Pancreas_OC	pancreas:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
44	CTCF	chr21:40813540-40813697	MCF-7	breast:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
45	CTCF	chr21:40813497-40813763	K562	blood:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
46	CTCF	chr21:40813519-40813735	GM20000	blood:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
47	CTCF	chr21:40813523-40813748	GM10248	blood:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
48	SMC3	chr21:40813356-40813822	K562	blood:	n/a	n/a
49	CTCF	chr21:40813512-40813742	ProgFib	skin:	n/a	chr21:40813610-40813631 chr21:40813615-40813633
50	CTCF	chr21:40813500-40813748	LNCaP	prostate:	n/a	chr21:40813610-40813631 chr21:40813615-40813633

No.	Distal block	Cell Line	Cell type
1	chr21:40791594..40793834-chr21:40813541..40816112,2	K562	blood:
2	chr21:40806088..40810379-chr21:40811300..40813801,4	MCF-7	breast:
3	chr21:40759186..40760805-chr21:40811887..40813577,2	K562	blood:
4	chr21:40177677..40179381-chr21:40812548..40814050,2	K562	blood:
5	chr21:40683646..40687466-chr21:40813293..40816602,5	MCF-7	breast:
6	chr21:40745299..40746167-chr21:40813543..40814094,2	MCF-7	breast:
7	chr21:40808402..40815127-chr21:40815513..40821149,12	K562	blood:
8	chr21:40757952..40760815-chr21:40812863..40817486,4	MCF-7	breast:
9	21:40748850-40752541..21:40812812-40815481	K562	blood:
10	chr21:40812406..40815051-chr21:40815498..40817690,4	K562	blood:
11	chr21:40808329..40812009-chr21:40812185..40815067,5	K562	blood:
12	chr21:40719600..40723122-chr21:40811701..40815528,3	K562	blood:
13	chr21:40768684..40769218-chr21:40813214..40814049,2	MCF-7	breast:
14	chr21:40685795..40687913-chr21:40812651..40815254,2	K562	blood:
15	chr21:40760487..40761081-chr21:40813246..40814131,2	MCF-7	breast:
16	chr21:40760349..40761906-chr21:40811512..40813865,2	K562	blood:

Variant related genes	Relation type
LCA5L	TF binding region
SH3BGR	TF binding region
ENSG00000227406	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000157557	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000255568	Chromatin interaction
ENSG00000238141	Chromatin interaction
ENSG00000157578	Chromatin interaction
ENSG00000185658	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11575939	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16997618	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2063998	0.84[YRI][hapmap]
rs2065313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2223028	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410128	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837009	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837015	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837017	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837020	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2837021	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837022	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2837023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837029	1.00[CEU][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837034	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837036	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281987	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56812456	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56866897	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58900137	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596289	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs61342945	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7275686	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7276575	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7276981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7279753	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73365952	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73367928	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367962	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367974	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367976	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73906032	0.81[ASN][1000 genomes]
rs73906033	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73906034	0.81[ASN][1000 genomes]
rs940625	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9680443	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7277627	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs7277627	WRB	cis	lung	GTEx
rs7277627	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs7277627	LCA5L	cis	Artery Tibial	GTEx
rs7277627	WRB	cis	Nerve Tibial	GTEx
rs7277627	SH3BGR	cis	Artery Tibial	GTEx
rs7277627	LCA5L	cis	Esophagus Muscularis	GTEx
rs7277627	WRB	cis	Artery Tibial	GTEx
rs7277627	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs7277627	LCA5L	cis	lung	GTEx
rs7277627	LCA5L	cis	Artery Aorta	GTEx
rs7277627	LCA5L	cis	Thyroid	GTEx
rs7277627	WRB	cis	Adipose Subcutaneous	GTEx
rs7277627	LCA5L	cis	Nerve Tibial	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40778200-40816600	Weak transcription	Pancreas	Pancrea
2	chr21:40778400-40816600	Weak transcription	Left Ventricle	heart
3	chr21:40802000-40813800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr21:40802600-40816200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr21:40802600-40816600	Weak transcription	Right Atrium	heart
6	chr21:40802800-40814000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:40809200-40813800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr21:40809400-40816400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr21:40809800-40816600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr21:40811600-40816600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr21:40812600-40816600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr21:40813000-40814800	Enhancers	HSMM	muscle
13	chr21:40813000-40815400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr21:40813200-40813800	Enhancers	HSMMtube	muscle
15	chr21:40813400-40814000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr21:40813400-40814000	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr21:40813400-40816400	Weak transcription	Hela-S3	cervix

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