Variant report

Variant	rs2993261
Chromosome Location	chr1:46009353-46009354
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45986741..45989512-chr1:46009313..46013712,6	MCF-7	breast:
2	chr1:45982342..45989534-chr1:46006947..46020678,57	K562	blood:
3	chr1:45998915..46004761-chr1:46006522..46011880,8	K562	blood:
4	chr1:45977514..45980437-chr1:46009344..46010856,2	K562	blood:
5	chr1:45976870..45989534-chr1:46007918..46019226,54	K562	blood:
6	chr1:46006129..46009713-chr1:46009736..46013035,4	K562	blood:
7	chr1:46008208..46011176-chr1:46015196..46017542,3	MCF-7	breast:
8	chr1:46007470..46009634-chr1:46048719..46050358,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000117450	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000132780	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11211125	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211127	1.00[EUR][1000 genomes]
rs12065695	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066809	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12067882	1.00[EUR][1000 genomes]
rs12070890	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073047	1.00[EUR][1000 genomes]
rs12083690	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091335	1.00[EUR][1000 genomes]
rs12093444	1.00[EUR][1000 genomes]
rs12565230	1.00[EUR][1000 genomes]
rs16832540	1.00[EUR][1000 genomes]
rs16832545	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16832550	1.00[EUR][1000 genomes]
rs16832557	1.00[EUR][1000 genomes]
rs16832559	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1855621	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28532613	1.00[EUR][1000 genomes]
rs28674795	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2934860	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934861	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934863	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2934864	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991965	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2991967	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2991984	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2993256	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2993260	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014222	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014223	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014224	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014226	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35067820	1.00[EUR][1000 genomes]
rs35103566	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36053912	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57910611	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59050426	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60347972	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60660559	1.00[EUR][1000 genomes]
rs6664588	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671347	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677135	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699702	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72478602	1.00[ASN][1000 genomes]
rs72480603	1.00[ASN][1000 genomes]
rs72896187	1.00[EUR][1000 genomes]
rs72898313	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72898315	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72898320	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72898323	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900311	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7412911	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7536559	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550744	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429080	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429083	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429164	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9429165	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46000800-46016000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:46002600-46009600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:46006400-46009400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:46006400-46009400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:46006400-46012200	Enhancers	Primary B cells from peripheral blood	blood
6	chr1:46006800-46009800	Enhancers	Primary hematopoietic stem cells	blood
7	chr1:46006800-46012200	Enhancers	Fetal Intestine Small	intestine
8	chr1:46007000-46009400	Enhancers	Primary B cells from cord blood	blood
9	chr1:46007200-46013600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:46007400-46011800	Enhancers	Stomach Mucosa	stomach
11	chr1:46007600-46012000	Enhancers	Fetal Intestine Large	intestine
12	chr1:46007800-46009600	Enhancers	Adipose Nuclei	Adipose
13	chr1:46008000-46010000	Enhancers	K562	blood
14	chr1:46008000-46010200	Weak transcription	Placenta	Placenta
15	chr1:46008200-46009400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:46008200-46009400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:46008200-46009400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:46008200-46009600	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr1:46008200-46010000	Enhancers	Pancreas	Pancrea
20	chr1:46008200-46010200	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr1:46008200-46010400	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr1:46008200-46011000	Enhancers	Spleen	Spleen
23	chr1:46008200-46011400	Enhancers	Primary T cells fromperipheralblood	blood
24	chr1:46008200-46012200	Enhancers	Fetal Thymus	thymus
25	chr1:46008400-46009400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr1:46008400-46009400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr1:46008400-46009400	Enhancers	HUVEC	blood vessel
28	chr1:46008400-46009800	Enhancers	Right Atrium	heart
29	chr1:46008400-46011400	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr1:46008600-46009600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:46008600-46009600	Weak transcription	Lung	lung
32	chr1:46008600-46011600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:46008800-46009400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr1:46008800-46009400	Enhancers	Thymus	Thymus
35	chr1:46008800-46009600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr1:46008800-46009600	Weak transcription	Colonic Mucosa	Colon
37	chr1:46009200-46009400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:46009200-46009400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:46009200-46009400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:46009200-46009400	Enhancers	Fetal Lung	lung
41	chr1:46009200-46009400	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr1:46009200-46009600	Flanking Active TSS	Liver	Liver
43	chr1:46009200-46009600	Bivalent Enhancer	NHDF-Ad	bronchial
44	chr1:46009200-46009800	Bivalent Enhancer	Fetal Muscle Leg	muscle
45	chr1:46009200-46010000	Enhancers	H1 Cell Line	embryonic stem cell
46	chr1:46009200-46010000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:46009200-46010000	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr1:46009200-46010000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:46009200-46010000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr1:46009200-46010000	Flanking Active TSS	Primary T cells from cord blood	blood

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