Variant report

Variant	rs16828700
Chromosome Location	chr2:149266954-149266955
allele	G/T
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	chr2:148747086..148748063-chr2:149266705..149267668,7	MCF-7	breast:
2	chr2:148695019..148695866-chr2:149266727..149267624,3	K562	blood:
3	chr2:148967081..148967666-chr2:149266757..149267493,2	MCF-7	breast:
4	chr2:149257990..149260894-chr2:149265586..149267154,2	K562	blood:
5	chr2:148777185..148777981-chr2:149266660..149267608,2	MCF-7	breast:
6	chr2:148925257..148925927-chr2:149266799..149267551,3	MCF-7	breast:
7	chr2:148747289..148748018-chr2:149266484..149267635,9	MCF-7	breast:
8	chr2:148685824..148687356-chr2:149266124..149268743,2	K562	blood:
9	chr2:148746863..148748075-chr2:149266691..149267630,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115947	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs13008472	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010376	0.87[ASN][1000 genomes]
rs13014173	0.87[ASN][1000 genomes]
rs13033892	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13034925	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17357225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17357457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979038	0.87[ASN][1000 genomes]
rs2197581	0.87[ASN][1000 genomes]
rs4972280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6751753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71350081	0.87[ASN][1000 genomes]
rs71413618	0.87[ASN][1000 genomes]
rs71413619	0.87[ASN][1000 genomes]
rs71413620	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs765056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs940460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[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	esv2753542	chr2:149004714-149268503	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1012275	chr2:149031668-149316793	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv2751831	chr2:149151358-150105603	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1000101	chr2:149165813-149361220	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer 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	5 gene(s)	inside rSNPs	diseases
5	nsv868861	chr2:149198443-149434604	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv917109	chr2:149198443-149948302	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1004663	chr2:149214090-149373061	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv2762913	chr2:149249683-149345487	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16828700	GSTM3	trans	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:149247600-149291000	Weak transcription	Spleen	Spleen
2	chr2:149248600-149267000	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:149248800-149267000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:149248800-149269600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:149248800-149276800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:149248800-149284600	Weak transcription	Lung	lung
7	chr2:149259400-149267000	Weak transcription	Gastric	stomach
8	chr2:149259600-149267000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:149261600-149279200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:149264200-149267000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:149265600-149267600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr2:149266200-149267600	Flanking Active TSS	HepG2	liver
13	chr2:149266400-149267600	Active TSS	Aorta	Aorta
14	chr2:149266600-149267000	Enhancers	H1 Cell Line	embryonic stem cell
15	chr2:149266600-149267000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:149266600-149267000	Flanking Active TSS	Osteobl	bone
17	chr2:149266600-149267200	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr2:149266600-149267200	Active TSS	GM12878-XiMat	blood
19	chr2:149266600-149267200	Flanking Active TSS	K562	blood
20	chr2:149266600-149267200	Active TSS	NHEK	skin
21	chr2:149266600-149267400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr2:149266600-149267400	Enhancers	Fetal Brain Male	brain
23	chr2:149266600-149267400	Active TSS	Rectal Smooth Muscle	rectum
24	chr2:149266600-149267400	Active TSS	A549	lung
25	chr2:149266600-149267600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr2:149266600-149267600	Enhancers	Colon Smooth Muscle	Colon
27	chr2:149266600-149268000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:149266800-149267000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr2:149266800-149267000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr2:149266800-149267000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr2:149266800-149267000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:149266800-149267000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:149266800-149267000	Active TSS	Primary B cells from cord blood	blood
34	chr2:149266800-149267000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr2:149266800-149267000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr2:149266800-149267000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:149266800-149267000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:149266800-149267000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:149266800-149267000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:149266800-149267000	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr2:149266800-149267000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr2:149266800-149267000	Enhancers	Placenta Amnion	Placenta Amnion
43	chr2:149266800-149267000	Enhancers	Right Ventricle	heart
44	chr2:149266800-149267000	Active TSS	Thymus	Thymus
45	chr2:149266800-149267000	Flanking Active TSS	HSMM	muscle
46	chr2:149266800-149267000	Active TSS	HSMMtube	muscle
47	chr2:149266800-149267000	Flanking Active TSS	HUVEC	blood vessel
48	chr2:149266800-149267000	Active TSS	Monocytes-CD14+_RO01746	blood
49	chr2:149266800-149267000	Flanking Active TSS	NH-A	brain
50	chr2:149266800-149267200	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links