Variant report

Variant	rs1188976
Chromosome Location	chr1:228261901-228261902
allele	C/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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228191745..228192555-chr1:228261259..228261971,3	MCF-7	breast:
2	chr1:228193335..228195504-chr1:228260630..228262645,2	MCF-7	breast:
3	chr1:227946633..227949211-chr1:228261877..228264518,2	K562	blood:
4	chr1:228248925..228252171-chr1:228258918..228261969,3	MCF-7	breast:
5	chr1:228191736..228192588-chr1:228261257..228262099,3	K562	blood:
6	chr1:228191984..228194843-chr1:228260469..228263373,2	MCF-7	breast:
7	chr1:228190941..228192847-chr1:228260763..228262214,8	MCF-7	breast:
8	chr1:228230050..228232873-chr1:228260583..228263014,2	MCF-7	breast:
9	chr1:228186931..228189875-chr1:228260382..228263090,3	MCF-7	breast:
10	chr1:228261534..228262217-chr1:228318541..228319233,2	MCF-7	breast:
11	chr1:228187251..228191319-chr1:228259829..228263819,5	MCF-7	breast:
12	chr1:228196561..228199539-chr1:228260175..228262293,2	MCF-7	breast:
13	chr1:227949923..227950798-chr1:228261303..228262101,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000154342	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10916269	0.85[ASW][hapmap];0.91[LWK][hapmap]
rs1094601	0.91[AMR][1000 genomes]
rs1771465	0.89[AFR][1000 genomes]
rs1771475	0.85[ASW][hapmap];0.94[LWK][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs73092925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73110782	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs822728	0.85[ASW][hapmap];0.94[LWK][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs822729	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs822730	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs822731	0.85[ASW][hapmap];0.94[LWK][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs822735	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs822737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822742	0.91[AMR][1000 genomes]
rs849750	0.85[ASW][hapmap];0.94[LWK][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
9	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	91 gene(s)	inside rSNPs	diseases
11	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228248200-228269000	Weak transcription	Right Atrium	heart
2	chr1:228258600-228269000	Weak transcription	Esophagus	oesophagus
3	chr1:228259600-228262000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:228260200-228268000	Weak transcription	Gastric	stomach
5	chr1:228260200-228269000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:228260800-228262000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:228260800-228262200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr1:228260800-228262200	Enhancers	Brain Germinal Matrix	brain
9	chr1:228261000-228262200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:228261000-228262200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:228261000-228262200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:228261000-228262400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr1:228261000-228263200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:228261000-228263400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:228261200-228262200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:228261200-228262200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:228261200-228262200	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr1:228261200-228263000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:228261200-228267600	Weak transcription	Ovary	ovary
20	chr1:228261400-228262000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
21	chr1:228261400-228262000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
22	chr1:228261400-228262000	Enhancers	Placenta	Placenta
23	chr1:228261400-228262000	Enhancers	Lung	lung
24	chr1:228261400-228262000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
25	chr1:228261600-228269000	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:228261800-228262000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
27	chr1:228261800-228262000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:228261800-228262000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:228261800-228262000	Enhancers	Spleen	Spleen
30	chr1:228261800-228262200	Enhancers	Fetal Brain Female	brain

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