Variant report

Variant	rs28370020
Chromosome Location	chr1:223904606-223904607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223903451..223905300-chr1:223920938..223923297,2	MCF-7	breast:
2	chr1:223891592..223893967-chr1:223903233..223904840,2	K562	blood:
3	chr1:223903418..223905687-chr1:223928822..223931791,2	MCF-7	breast:
4	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
5	chr1:223904423..223906015-chr1:223946207..223948782,2	K562	blood:
6	chr1:223904247..223905976-chr1:223916920..223919197,2	MCF-7	breast:
7	chr1:223895202..223897591-chr1:223904463..223906328,2	K562	blood:

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10916601	0.96[ASN][1000 genomes]
rs10916602	0.96[ASN][1000 genomes]
rs10916604	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11579787	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11580689	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11581716	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11588475	0.90[EUR][1000 genomes]
rs12057708	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12074091	0.96[ASN][1000 genomes]
rs12080565	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16842040	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs16842062	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1892077	0.96[ASN][1000 genomes]
rs2000320	0.92[ASN][1000 genomes]
rs2154113	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2154114	0.81[ASN][1000 genomes]
rs2186006	0.96[ASN][1000 genomes]
rs2275877	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28370012	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28370013	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28370014	0.96[ASN][1000 genomes]
rs28370029	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4653499	0.96[ASN][1000 genomes]
rs61823966	0.96[ASN][1000 genomes]
rs6669046	0.82[ASN][1000 genomes]
rs6674733	0.82[ASN][1000 genomes]
rs7366009	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7414311	0.96[ASN][1000 genomes]
rs7555491	0.96[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	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	nsv437346	chr1:223903781-223905532	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223900800-223906000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:223901000-223905200	Enhancers	Spleen	Spleen
3	chr1:223901000-223905800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr1:223901200-223904800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:223901200-223905400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:223901400-223904800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
7	chr1:223901400-223905600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:223901400-223907600	Transcr. at gene 5' and 3'	A549	lung
9	chr1:223901600-223905200	Transcr. at gene 5' and 3'	NHEK	skin
10	chr1:223901600-223905800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:223901600-223906200	Enhancers	Primary B cells from peripheral blood	blood
12	chr1:223901600-223906400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:223901800-223904800	Enhancers	Fetal Brain Female	brain
14	chr1:223901800-223905000	Enhancers	Fetal Heart	heart
15	chr1:223901800-223905000	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr1:223901800-223905200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr1:223901800-223905600	Genic enhancers	Fetal Muscle Trunk	muscle
18	chr1:223901800-223905800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:223901800-223906200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr1:223902000-223905000	Enhancers	Fetal Brain Male	brain
21	chr1:223902200-223904800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:223902200-223904800	Genic enhancers	Fetal Stomach	stomach
23	chr1:223902200-223905200	Genic enhancers	Fetal Muscle Leg	muscle
24	chr1:223902200-223913400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:223902400-223905800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:223902400-223906200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:223902400-223906600	Enhancers	Fetal Thymus	thymus
28	chr1:223902600-223904800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:223902600-223904800	Enhancers	Stomach Mucosa	stomach
30	chr1:223902600-223904800	Flanking Active TSS	HSMMtube	muscle
31	chr1:223902600-223905000	Enhancers	Gastric	stomach
32	chr1:223902600-223905000	Flanking Active TSS	GM12878-XiMat	blood
33	chr1:223902600-223905200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr1:223902600-223905400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr1:223902600-223906000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:223902800-223904800	Enhancers	Psoas Muscle	Psoas
37	chr1:223902800-223905000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:223902800-223914200	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:223903000-223905000	Genic enhancers	Colon Smooth Muscle	Colon
40	chr1:223903000-223905800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:223903000-223906000	Enhancers	Primary B cells from cord blood	blood
42	chr1:223903000-223907800	Weak transcription	Liver	Liver
43	chr1:223903200-223906400	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr1:223903200-223907200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:223903200-223913600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:223903400-223905000	Weak transcription	Right Ventricle	heart
47	chr1:223903400-223905200	Weak transcription	Pancreas	Pancrea
48	chr1:223903400-223906200	Strong transcription	Fetal Kidney	kidney
49	chr1:223903400-223907400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
50	chr1:223903400-223908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links