Variant report

Variant	rs72677567
Chromosome Location	chr1:46636888-46636889
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	FOXM1	chr1:46636779-46637972	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr1:46636691-46638495	ECC-1	luminal epithelium:	n/a	n/a
3	GABPA	chr1:46636866-46637417	MCF-7	breast:	n/a	n/a
4	MAX	chr1:46636882-46638504	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr1:46636735-46638519	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr1:46636699-46638570	ECC-1	luminal epithelium:	n/a	chr1:46637847-46637856 chr1:46637179-46637186
7	ZBTB7A	chr1:46636848-46638085	ECC-1	luminal epithelium:	n/a	n/a
8	GABPA	chr1:46636722-46638105	MCF-7	breast:	n/a	n/a
9	RAD21	chr1:46636858-46638424	ECC-1	luminal epithelium:	n/a	n/a
10	TEAD4	chr1:46636639-46638428	ECC-1	luminal epithelium:	n/a	n/a
11	TEAD4	chr1:46636875-46638326	ECC-1	luminal epithelium:	n/a	n/a
12	TFAP2A	chr1:46636845-46637935	Hela-S3	cervix:	n/a	chr1:46637703-46637717 chr1:46637298-46637310 chr1:46637705-46637715 chr1:46637286-46637301 chr1:46637705-46637715 chr1:46637296-46637310 chr1:46637298-46637310 chr1:46637705-46637715 chr1:46637705-46637715 chr1:46637298-46637310 chr1:46637298-46637310
13	TCF12	chr1:46636845-46638556	ECC-1	luminal epithelium:	n/a	n/a
14	EP300	chr1:46636871-46638061	ECC-1	luminal epithelium:	n/a	chr1:46637847-46637856 chr1:46637179-46637186
15	NFIC	chr1:46636686-46638436	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:46635040..46637380-chr1:46652840..46654559,2	MCF-7	breast:
2	chr1:46621624..46623381-chr1:46635953..46637787,2	MCF-7	breast:
3	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
4	chr1:46636028..46638246-chr1:46712360..46714250,2	MCF-7	breast:
5	chr1:46636439..46638004-chr1:46642025..46643835,2	MCF-7	breast:
6	chr1:46636697..46639165-chr1:46652056..46653716,2	MCF-7	breast:
7	chr1:46635707..46641847-chr1:46658318..46665376,6	K562	blood:
8	chr1:46636220..46637897-chr1:46645659..46648862,3	MCF-7	breast:
9	chr1:46619572..46621835-chr1:46635358..46637893,2	MCF-7	breast:
10	chr1:46636119..46638195-chr2:81815588..81817410,2	MCF-7	breast:
11	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:
12	chr1:46630846..46632404-chr1:46635981..46638710,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POMGNT1-3	chr1:46636736-46637060	NONHSAT002987

Variant related genes	Relation type
TSPAN1	TF binding region
ENSG00000117461	Chromatin interaction
ENSG00000227857	Chromatin interaction
ENSG00000085999	Chromatin interaction
ENSG00000250719	Chromatin interaction
ENSG00000085998	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12076680	1.00[ASN][1000 genomes]
rs12123115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131635	0.98[EUR][1000 genomes]
rs55884940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9660699	0.86[AMR][1000 genomes];0.98[EUR][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	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46633200-46637000	Weak transcription	Esophagus	oesophagus
2	chr1:46633200-46637000	Weak transcription	Pancreas	Pancrea
3	chr1:46633200-46637000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:46633200-46637600	Weak transcription	Psoas Muscle	Psoas
5	chr1:46633400-46637200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr1:46633400-46637800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:46633400-46638800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:46633400-46638800	Weak transcription	Brain Anterior Caudate	brain
9	chr1:46633400-46638800	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:46633400-46638800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:46633600-46639200	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr1:46634400-46638800	Weak transcription	K562	blood
13	chr1:46635600-46642200	Enhancers	Lung	lung
14	chr1:46636600-46638000	Enhancers	HMEC	breast
15	chr1:46636800-46637000	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr1:46636800-46637000	Bivalent Enhancer	NHEK	skin
17	chr1:46636800-46637200	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr1:46636800-46637400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
19	chr1:46636800-46637400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr1:46636800-46637400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr1:46636800-46637400	Enhancers	GM12878-XiMat	blood
22	chr1:46636800-46637400	Enhancers	HSMM	muscle
23	chr1:46636800-46637600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:46636800-46637600	Enhancers	HUVEC	blood vessel
25	chr1:46636800-46637800	Enhancers	Fetal Thymus	thymus
26	chr1:46636800-46637800	Flanking Active TSS	Hela-S3	cervix
27	chr1:46636800-46638000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:46636800-46638000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:46636800-46638000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:46636800-46638000	Enhancers	Fetal Lung	lung
31	chr1:46636800-46638000	Enhancers	Gastric	stomach
32	chr1:46636800-46638000	Enhancers	Stomach Mucosa	stomach
33	chr1:46636800-46638000	Enhancers	Spleen	Spleen
34	chr1:46636800-46638200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:46636800-46638200	Enhancers	Primary B cells from peripheral blood	blood
36	chr1:46636800-46639400	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr1:46636800-46641200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:46636800-46641400	Enhancers	Placenta	Placenta
39	chr1:46636800-46642200	Enhancers	Left Ventricle	heart
40	chr1:46636800-46642400	Enhancers	Right Atrium	heart
41	chr1:46636800-46642400	Enhancers	Right Ventricle	heart

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