Variant report

Variant	rs41270177
Chromosome Location	chr1:228248508-228248509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228241440..228243114-chr1:228247726..228249547,2	MCF-7	breast:
2	chr1:228193180..228197909-chr1:228245616..228249822,4	MCF-7	breast:
3	chr1:228185813..228188454-chr1:228247740..228249945,2	MCF-7	breast:
4	chr1:228246811..228249127-chr1:228257869..228259965,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154342	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1034792	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1048503	0.84[EUR][1000 genomes]
rs10916261	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10916262	0.98[EUR][1000 genomes]
rs1094602	0.82[ASN][1000 genomes]
rs11582265	0.82[EUR][1000 genomes]
rs11582704	0.82[EUR][1000 genomes]
rs11584499	0.96[EUR][1000 genomes]
rs11589513	0.98[EUR][1000 genomes]
rs1188975	0.99[ASN][1000 genomes]
rs1188977	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12033088	1.00[EUR][1000 genomes]
rs12048010	0.98[EUR][1000 genomes]
rs13374948	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1620734	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1745420	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1745422	1.00[EUR][1000 genomes]
rs2070960	0.84[EUR][1000 genomes]
rs2107905	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3738680	0.84[EUR][1000 genomes]
rs3738681	0.84[EUR][1000 genomes]
rs3768329	0.82[EUR][1000 genomes]
rs3768330	0.82[EUR][1000 genomes]
rs3820624	0.82[EUR][1000 genomes]
rs41270175	1.00[EUR][1000 genomes]
rs4363416	0.83[EUR][1000 genomes]
rs4653897	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57146523	0.98[EUR][1000 genomes]
rs57657087	0.98[EUR][1000 genomes]
rs60213528	0.83[EUR][1000 genomes]
rs61825125	0.84[EUR][1000 genomes]
rs61825130	0.98[EUR][1000 genomes]
rs61825131	1.00[EUR][1000 genomes]
rs61825133	0.94[EUR][1000 genomes]
rs6672422	0.81[EUR][1000 genomes]
rs6672601	0.81[EUR][1000 genomes]
rs708126	0.99[ASN][1000 genomes]
rs72756204	0.98[EUR][1000 genomes]
rs72756209	0.94[EUR][1000 genomes]
rs7530812	0.81[EUR][1000 genomes]
rs7539664	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs822727	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs860301	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs882451	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	esv1814215	chr1:228231601-228259932	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
10	esv1844252	chr1:228231601-228259932	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
11	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
12	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

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228246200-228248800	ZNF genes & repeats	Spleen	Spleen
2	chr1:228246600-228249000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:228246600-228249000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr1:228246600-228249000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr1:228246600-228249000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr1:228246800-228248600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
7	chr1:228246800-228249000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr1:228247000-228248600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
9	chr1:228247000-228248600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
10	chr1:228247000-228248800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:228247000-228249000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
12	chr1:228247200-228248600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
13	chr1:228247200-228248600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
14	chr1:228247200-228248600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
15	chr1:228247200-228248800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr1:228247200-228248800	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr1:228247200-228248800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
18	chr1:228247200-228249000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr1:228247400-228248600	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr1:228247400-228248600	Active TSS	Hela-S3	cervix
21	chr1:228247400-228248800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
22	chr1:228247600-228248600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
23	chr1:228247600-228248600	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach
24	chr1:228247600-228248800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:228247600-228248800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:228247600-228248800	Bivalent Enhancer	Fetal Muscle Leg	muscle
27	chr1:228247600-228249000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:228247800-228248600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:228247800-228248600	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
30	chr1:228247800-228248600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
31	chr1:228247800-228248600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
32	chr1:228247800-228248600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
33	chr1:228247800-228248600	Flanking Active TSS	K562	blood
34	chr1:228247800-228248800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
35	chr1:228247800-228248800	Bivalent Enhancer	Placenta	Placenta
36	chr1:228248000-228248600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:228248000-228248600	Bivalent Enhancer	Brain Substantia Nigra	brain
38	chr1:228248000-228248600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
39	chr1:228248000-228248600	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
40	chr1:228248000-228248600	Flanking Bivalent TSS/Enh	NHEK	skin
41	chr1:228248000-228248800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:228248000-228248800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:228248000-228248800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
44	chr1:228248000-228249000	Bivalent Enhancer	Primary B cells from cord blood	blood
45	chr1:228248000-228249000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
46	chr1:228248000-228249000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:228248000-228249200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:228248200-228248600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:228248200-228248600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr1:228248200-228248600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood

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