Variant report

Variant	rs12078927
Chromosome Location	chr1:228875686-228875687
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	RAD21	chr1:228875122-228875780	MCF-7	breast:	n/a	n/a
2	RAD21	chr1:228875095-228875755	MCF-7	breast:	n/a	n/a
3	SIN3AK20	chr1:228874877-228875767	MCF-7	breast:	n/a	n/a
4	SIN3AK20	chr1:228874943-228875712	MCF-7	breast:	n/a	n/a
5	ELF1	chr1:228875140-228875721	MCF-7	breast:	n/a	chr1:228875404-228875415
6	RAD21	chr1:228875273-228875702	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228875351..228875980-chr1:229362943..229363511,2	MCF-7	breast:
2	chr1:228874211..228876992-chr1:228882867..228885336,2	K562	blood:

Variant related genes	Relation type
RHOU	TF binding region
ENSG00000233920	Chromatin interaction

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]
rs12077418	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:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228872400-228876400	Weak transcription	Hela-S3	cervix
2	chr1:228872400-228880200	Weak transcription	Left Ventricle	heart
3	chr1:228872600-228877800	Weak transcription	Primary T cells from cord blood	blood
4	chr1:228872600-228878400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:228872600-228880600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:228872600-228881200	Weak transcription	Esophagus	oesophagus
7	chr1:228872600-228884400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:228873000-228875800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:228873200-228878400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:228873200-228879000	Weak transcription	Ovary	ovary
11	chr1:228873200-228884800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:228873400-228876400	Weak transcription	Fetal Kidney	kidney
13	chr1:228873400-228876400	Enhancers	Stomach Mucosa	stomach
14	chr1:228873400-228879000	Weak transcription	Small Intestine	intestine
15	chr1:228873600-228876000	Transcr. at gene 5' and 3'	Brain Substantia Nigra	brain
16	chr1:228873600-228876200	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:228873600-228876600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:228873600-228876600	Genic enhancers	Pancreas	Pancrea
19	chr1:228873600-228877000	Genic enhancers	HepG2	liver
20	chr1:228873600-228877200	Genic enhancers	Fetal Thymus	thymus
21	chr1:228873600-228878000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:228873600-228878000	Weak transcription	Brain Germinal Matrix	brain
23	chr1:228873600-228878400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:228873600-228878400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:228873600-228879000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:228873600-228879000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:228873800-228875800	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr1:228873800-228876600	Genic enhancers	Stomach Smooth Muscle	stomach
29	chr1:228873800-228877200	Genic enhancers	Fetal Intestine Large	intestine
30	chr1:228873800-228878400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:228873800-228878600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr1:228873800-228879000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr1:228873800-228879000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:228873800-228879000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:228873800-228880200	Weak transcription	Thymus	Thymus
36	chr1:228873800-228882800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:228873800-228884200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:228873800-228884200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:228874000-228875800	Genic enhancers	Aorta	Aorta
40	chr1:228874000-228876400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr1:228874000-228876600	Genic enhancers	Primary monocytes fromperipheralblood	blood
42	chr1:228874000-228877200	Genic enhancers	Spleen	Spleen
43	chr1:228874000-228879200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:228874000-228879400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:228874000-228881800	Genic enhancers	Liver	Liver
46	chr1:228874200-228875800	Genic enhancers	Monocytes-CD14+_RO01746	blood
47	chr1:228874200-228876600	Genic enhancers	Placenta	Placenta
48	chr1:228874200-228877400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr1:228874200-228878000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:228874200-228880400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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