Variant report

Variant	rs2991969
Chromosome Location	chr1:46009969-46009970
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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:

Variant related genes	Relation type
ENSG00000117450	Chromatin interaction
ENSG00000117448	Chromatin interaction

Extended variants
information (count: 65 )
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]
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]
rs2993261	1.00[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:6 , 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	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
3	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
4	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
5	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
6	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:83 , 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	chr1:46006400-46012200	Enhancers	Primary B cells from peripheral blood	blood
3	chr1:46006800-46012200	Enhancers	Fetal Intestine Small	intestine
4	chr1:46007200-46013600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:46007400-46011800	Enhancers	Stomach Mucosa	stomach
6	chr1:46007600-46012000	Enhancers	Fetal Intestine Large	intestine
7	chr1:46008000-46010000	Enhancers	K562	blood
8	chr1:46008000-46010200	Weak transcription	Placenta	Placenta
9	chr1:46008200-46010000	Enhancers	Pancreas	Pancrea
10	chr1:46008200-46010200	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr1:46008200-46010400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr1:46008200-46011000	Enhancers	Spleen	Spleen
13	chr1:46008200-46011400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:46008200-46012200	Enhancers	Fetal Thymus	thymus
15	chr1:46008400-46011400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:46008600-46011600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:46009200-46010000	Enhancers	H1 Cell Line	embryonic stem cell
18	chr1:46009200-46010000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:46009200-46010000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr1:46009200-46010000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:46009200-46010000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr1:46009200-46010000	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr1:46009200-46010000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr1:46009200-46010000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:46009200-46010000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr1:46009200-46010000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:46009200-46010000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:46009200-46010000	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr1:46009200-46010000	Enhancers	Gastric	stomach
30	chr1:46009200-46010000	Flanking Active TSS	Dnd41	blood
31	chr1:46009200-46010000	Enhancers	HSMM	muscle
32	chr1:46009200-46010000	Flanking Active TSS	Osteobl	bone
33	chr1:46009200-46010200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:46009200-46010200	Enhancers	Small Intestine	intestine
35	chr1:46009200-46010800	Enhancers	Esophagus	oesophagus
36	chr1:46009200-46011000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr1:46009200-46011400	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr1:46009200-46011400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr1:46009200-46011600	Flanking Active TSS	GM12878-XiMat	blood
40	chr1:46009200-46011800	Flanking Active TSS	HepG2	liver
41	chr1:46009400-46010000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr1:46009400-46010000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:46009400-46010000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:46009400-46010000	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr1:46009400-46010000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr1:46009400-46010000	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr1:46009400-46010000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr1:46009400-46010000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr1:46009400-46010000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:46009400-46010000	Enhancers	Duodenum Smooth Muscle	Duodenum

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