Variant report

Variant	rs16828096
Chromosome Location	chr2:148747902-148747903
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	chr2:148747393..148748097-chr2:149846190..149846982,2	MCF-7	breast:
2	chr2:148747119..148747979-chr2:148777459..148778023,2	MCF-7	breast:
3	chr2:148747178..148748066-chr2:148853587..148854325,3	MCF-7	breast:
4	chr2:148747086..148748063-chr2:149266705..149267668,7	MCF-7	breast:
5	chr2:148747445..148748127-chr2:149846144..149846862,2	K562	blood:
6	chr2:148746863..148748075-chr2:149266691..149267630,3	K562	blood:
7	chr2:148746466..148747928-chr2:148959011..148960040,7	MCF-7	breast:
8	chr2:148747289..148748018-chr2:149266484..149267635,9	MCF-7	breast:
9	chr2:148747741..148748520-chr2:149322760..149323458,2	K562	blood:

No data

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10187392	1.00[EUR][1000 genomes]
rs10497027	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10497030	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10928370	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12620026	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs13022827	1.00[CEU][hapmap]
rs13394568	1.00[EUR][1000 genomes]
rs13411618	1.00[EUR][1000 genomes]
rs1364659	1.00[EUR][1000 genomes]
rs1375858	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1469212	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16828024	1.00[EUR][1000 genomes]
rs16828025	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16828177	1.00[EUR][1000 genomes]
rs16828185	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16828243	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16828346	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16828388	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17218917	1.00[EUR][1000 genomes]
rs2627023	1.00[EUR][1000 genomes]
rs2627027	1.00[EUR][1000 genomes]
rs2707220	1.00[EUR][1000 genomes]
rs41468049	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4972314	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4972366	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs57204245	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58341690	1.00[EUR][1000 genomes]
rs60605559	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6430290	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6731167	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7578992	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7581537	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7600254	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916286	chr2:148438001-148977722	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv529388	chr2:148471340-148934846	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv3392562	chr2:148476961-148843061	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1009602	chr2:148668195-148844240	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv535967	chr2:148668195-148844240	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1000246	chr2:148669162-148780280	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv535968	chr2:148669162-148780280	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1002358	chr2:148703807-148942372	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1004169	chr2:148705700-148811850	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv535970	chr2:148705700-148811850	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1007683	chr2:148717347-148942372	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv535971	chr2:148717347-148942372	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv869326	chr2:148727068-148859804	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv817366	chr2:148727068-148879681	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1000852	chr2:148730825-148934986	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv535972	chr2:148730825-148934986	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv1009807	chr2:148731025-148829378	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv535973	chr2:148731025-148829378	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv1009696	chr2:148739650-148805668	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
20	nsv535974	chr2:148739650-148805668	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
21	nsv1011381	chr2:148739850-148805529	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
22	nsv535975	chr2:148739850-148805529	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
23	nsv999777	chr2:148740742-148809464	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
24	nsv916766	chr2:148743880-148955720	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
25	nsv1015003	chr2:148745734-148839653	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:148637200-148752600	Weak transcription	Small Intestine	intestine
2	chr2:148694200-148777400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr2:148709400-148776800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:148721400-148752800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:148721400-148763600	Weak transcription	Spleen	Spleen
6	chr2:148722800-148756400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:148726400-148752600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:148726600-148752600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:148728200-148773400	Weak transcription	K562	blood
10	chr2:148730800-148752600	Weak transcription	Primary T cells from cord blood	blood
11	chr2:148731400-148752800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:148736000-148776800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:148736200-148752000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:148736200-148752400	Weak transcription	Fetal Intestine Small	intestine
15	chr2:148736200-148752600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:148736200-148752800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:148736400-148750200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:148736400-148750400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:148736400-148750600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:148736400-148765600	Weak transcription	A549	lung
21	chr2:148736600-148752600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr2:148736600-148752600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:148737000-148753200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:148737600-148752600	Weak transcription	Primary B cells from cord blood	blood
25	chr2:148737600-148752600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:148739000-148750400	Weak transcription	Colon Smooth Muscle	Colon
27	chr2:148739000-148752600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:148739000-148759800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:148741200-148758000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:148741600-148755800	Weak transcription	Ovary	ovary
31	chr2:148741600-148756200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:148741800-148752800	Weak transcription	Thymus	Thymus
33	chr2:148741800-148757400	Weak transcription	Aorta	Aorta
34	chr2:148742200-148755800	Weak transcription	Gastric	stomach
35	chr2:148742400-148755800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:148742400-148756000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr2:148742800-148752800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:148743600-148757800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:148743600-148757800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr2:148744400-148754200	Weak transcription	HepG2	liver
41	chr2:148744600-148755800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr2:148746200-148752600	Weak transcription	Lung	lung
43	chr2:148746400-148748000	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr2:148746600-148748000	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr2:148746600-148748200	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr2:148746800-148748200	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr2:148746800-148748200	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr2:148747200-148748000	Enhancers	Fetal Lung	lung
49	chr2:148747200-148748000	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr2:148747200-148748200	Enhancers	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links