Variant report

Variant	rs2999159
Chromosome Location	chr1:113230758-113230759
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113183921..113186254-chr1:113229181..113230777,2	MCF-7	breast:
2	chr1:113226289..113228900-chr1:113228989..113230932,2	MCF-7	breast:
3	chr1:113214618..113222446-chr1:113227384..113233520,13	K562	blood:
4	chr1:113217617..113223835-chr1:113226384..113230990,8	MCF-7	breast:
5	chr1:113186005..113187624-chr1:113228785..113231335,2	K562	blood:
6	chr1:113214399..113219266-chr1:113227839..113232151,8	MCF-7	breast:
7	chr1:113230585..113232293-chr1:113255556..113258373,2	K562	blood:
8	chr1:113229049..113232047-chr1:113233162..113235859,4	MCF-7	breast:
9	chr1:113161141..113162992-chr1:113229521..113231702,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000261595	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000116489	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12126494	1.00[ASN][1000 genomes]
rs12750621	0.95[ASN][1000 genomes]
rs2279500	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932529	0.84[ASN][1000 genomes]
rs2932537	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999158	0.86[AFR][1000 genomes]
rs3013433	1.00[ASN][1000 genomes]
rs35221527	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
5	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113218400-113234200	Weak transcription	Aorta	Aorta
2	chr1:113218600-113232200	Weak transcription	Ovary	ovary
3	chr1:113218600-113235000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:113218600-113235400	Weak transcription	HSMM	muscle
5	chr1:113218600-113240800	Weak transcription	Right Atrium	heart
6	chr1:113218800-113232200	Weak transcription	Colonic Mucosa	Colon
7	chr1:113218800-113232400	Weak transcription	Brain Substantia Nigra	brain
8	chr1:113218800-113234200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:113219000-113231400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:113219000-113232000	Weak transcription	Hela-S3	cervix
11	chr1:113219000-113232200	Weak transcription	Small Intestine	intestine
12	chr1:113219000-113232400	Weak transcription	Brain Anterior Caudate	brain
13	chr1:113219000-113234400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:113219000-113235400	Weak transcription	A549	lung
15	chr1:113219000-113242200	Weak transcription	NHDF-Ad	bronchial
16	chr1:113219000-113243800	Weak transcription	Fetal Brain Male	brain
17	chr1:113219200-113230800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:113219200-113230800	Weak transcription	NHLF	lung
19	chr1:113219200-113232200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:113219200-113232400	Weak transcription	HUVEC	blood vessel
21	chr1:113219400-113231400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:113219400-113232600	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:113219400-113233200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:113219600-113231000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:113219600-113232000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:113219600-113232200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:113219600-113232600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:113219800-113231000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr1:113220000-113233000	Weak transcription	Primary B cells from cord blood	blood
30	chr1:113220000-113234400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:113220200-113231400	Weak transcription	Thymus	Thymus
32	chr1:113220200-113231600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr1:113220600-113231000	Weak transcription	Fetal Lung	lung
34	chr1:113220800-113232200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr1:113221200-113232200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:113222000-113243000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:113222200-113234200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:113224800-113235000	Weak transcription	HSMMtube	muscle
39	chr1:113226000-113231600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr1:113226000-113234200	Weak transcription	Pancreas	Pancrea
41	chr1:113226600-113230800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:113226800-113231400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:113228000-113231200	Weak transcription	Fetal Brain Female	brain
44	chr1:113228000-113234200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:113228200-113232400	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:113228400-113239000	Strong transcription	Fetal Intestine Small	intestine
47	chr1:113228600-113231200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:113228600-113242800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:113228600-113242800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:113228800-113231600	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links