Variant report

Variant	rs61521615
Chromosome Location	chr1:227949414-227949415
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227946182..227953403-chr1:228132950..228136592,12	MCF-7	breast:
2	chr1:227945386..227947892-chr1:227948405..227951247,3	MCF-7	breast:
3	chr1:227924939..227926521-chr1:227948276..227949805,2	MCF-7	breast:
4	chr1:227948959..227950844-chr1:228133923..228134938,14	MCF-7	breast:
5	chr1:227913567..227919162-chr1:227947935..227954215,6	MCF-7	breast:
6	chr1:227932601..227934786-chr1:227948065..227950535,2	MCF-7	breast:
7	chr1:227948352..227950485-chr1:227952945..227955700,2	MCF-7	breast:
8	chr1:227948805..227951027-chr1:227953567..227955861,2	MCF-7	breast:
9	chr1:227948596..227951213-chr1:228129640..228131293,2	MCF-7	breast:
10	chr1:227948253..227951244-chr1:228133555..228136345,5	MCF-7	breast:
11	chr1:227938992..227942354-chr1:227946217..227950282,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143816	Chromatin interaction
ENSG00000143740	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12064596	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2093611	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236358	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273938	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57892813	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674275	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688900	0.82[AMR][1000 genomes]
rs6695545	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs66969031	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67502955	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72632835	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72632836	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227924200-227955000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:227934400-227950000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:227934800-227950200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:227934800-227950400	Strong transcription	Fetal Intestine Small	intestine
5	chr1:227935000-227949600	Strong transcription	Dnd41	blood
6	chr1:227935200-227949800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:227937200-227949600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:227938000-227950200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:227938600-227950400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:227940400-227950000	Strong transcription	HepG2	liver
11	chr1:227940800-227949800	Strong transcription	Thymus	Thymus
12	chr1:227942000-227950000	Weak transcription	Small Intestine	intestine
13	chr1:227942600-227950000	Weak transcription	Stomach Mucosa	stomach
14	chr1:227943400-227949600	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:227943400-227949800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:227943600-227949800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:227943600-227949800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:227944000-227949800	Strong transcription	Brain Germinal Matrix	brain
19	chr1:227944000-227950400	Strong transcription	Fetal Intestine Large	intestine
20	chr1:227944000-227951800	Genic enhancers	Fetal Muscle Leg	muscle
21	chr1:227944200-227950000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:227944400-227949600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:227944600-227949800	Weak transcription	Hela-S3	cervix
24	chr1:227945000-227949800	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:227945400-227949600	Strong transcription	Primary B cells from cord blood	blood
26	chr1:227945600-227949600	Strong transcription	Brain Substantia Nigra	brain
27	chr1:227945800-227949800	Strong transcription	Aorta	Aorta
28	chr1:227945800-227954800	Weak transcription	Fetal Kidney	kidney
29	chr1:227946000-227949800	Strong transcription	Brain Hippocampus Middle	brain
30	chr1:227946000-227950600	Genic enhancers	GM12878-XiMat	blood
31	chr1:227946000-227960400	Strong transcription	Fetal Brain Female	brain
32	chr1:227946200-227950000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:227946400-227950000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:227946400-227950000	Strong transcription	Fetal Lung	lung
35	chr1:227946400-227950000	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:227946600-227949600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr1:227946600-227949600	Strong transcription	Adipose Nuclei	Adipose
38	chr1:227946600-227950000	Strong transcription	Lung	lung
39	chr1:227946800-227949600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr1:227946800-227950000	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr1:227946800-227952400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:227947000-227949600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr1:227947000-227949800	Strong transcription	Pancreas	Pancrea
44	chr1:227947400-227949600	Weak transcription	HMEC	breast
45	chr1:227947600-227949800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:227947600-227949800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:227947600-227954800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr1:227947800-227949600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:227947800-227949800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:227947800-227949800	Genic enhancers	HSMM	muscle

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