Variant report

Variant	rs12077418
Chromosome Location	chr1:228874494-228874495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228874211..228876992-chr1:228882867..228885336,2	K562	blood:
2	chr1:228827485..228830418-chr1:228872715..228875379,2	MCF-7	breast:
3	chr1:228872086..228874934-chr1:228877939..228879672,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1006797	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10489542	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1108502	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12059178	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12070785	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12075157	0.84[ASN][1000 genomes]
rs12076649	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12078927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12092986	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12096381	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1535129	0.97[EUR][1000 genomes]
rs2009564	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2180162	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2207704	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34036301	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806285	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3820265	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4654625	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6667385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681268	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7532644	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7554565	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013051	chr1:228786702-228903706	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv997801	chr1:228786702-228975127	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv870365	chr1:228788356-229267904	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv998255	chr1:228791784-228919202	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv549299	chr1:228793246-229455876	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv468316	chr1:228854703-228919202	Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv549300	chr1:228854703-228919202	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228870200-228875400	Active TSS	Brain Angular Gyrus	brain
2	chr1:228870600-228875400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:228872400-228875400	Weak transcription	Lung	lung
4	chr1:228872400-228875400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:228872400-228876400	Weak transcription	Hela-S3	cervix
6	chr1:228872400-228880200	Weak transcription	Left Ventricle	heart
7	chr1:228872600-228875400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:228872600-228877800	Weak transcription	Primary T cells from cord blood	blood
9	chr1:228872600-228878400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:228872600-228880600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:228872600-228881200	Weak transcription	Esophagus	oesophagus
12	chr1:228872600-228884400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr1:228873000-228874600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:228873000-228875800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:228873200-228878400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:228873200-228879000	Weak transcription	Ovary	ovary
17	chr1:228873200-228884800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:228873400-228874600	Transcr. at gene 5' and 3'	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:228873400-228876400	Weak transcription	Fetal Kidney	kidney
20	chr1:228873400-228876400	Enhancers	Stomach Mucosa	stomach
21	chr1:228873400-228879000	Weak transcription	Small Intestine	intestine
22	chr1:228873600-228875000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:228873600-228875400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:228873600-228875400	Weak transcription	Gastric	stomach
25	chr1:228873600-228875600	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
26	chr1:228873600-228876000	Transcr. at gene 5' and 3'	Brain Substantia Nigra	brain
27	chr1:228873600-228876200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:228873600-228876600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:228873600-228876600	Genic enhancers	Pancreas	Pancrea
30	chr1:228873600-228877000	Genic enhancers	HepG2	liver
31	chr1:228873600-228877200	Genic enhancers	Fetal Thymus	thymus
32	chr1:228873600-228878000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:228873600-228878000	Weak transcription	Brain Germinal Matrix	brain
34	chr1:228873600-228878400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr1:228873600-228878400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:228873600-228879000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:228873600-228879000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:228873800-228874600	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
39	chr1:228873800-228874600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr1:228873800-228874800	Genic enhancers	Primary T cells fromperipheralblood	blood
41	chr1:228873800-228875200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:228873800-228875400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:228873800-228875400	Weak transcription	Colonic Mucosa	Colon
44	chr1:228873800-228875400	Strong transcription	Fetal Stomach	stomach
45	chr1:228873800-228875800	Genic enhancers	Fetal Muscle Trunk	muscle
46	chr1:228873800-228876600	Genic enhancers	Stomach Smooth Muscle	stomach
47	chr1:228873800-228877200	Genic enhancers	Fetal Intestine Large	intestine
48	chr1:228873800-228878400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:228873800-228878600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr1:228873800-228879000	Weak transcription	H1 Cell Line	embryonic stem cell

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