Variant report

Variant	rs1724120
Chromosome Location	chr2:96809331-96809332
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:96808384..96810178-chr2:96817878..96819438,2	K562	blood:
2	chr2:96781378..96786213-chr2:96808688..96812498,6	MCF-7	breast:
3	chr2:96809057..96813419-chr2:96930542..96933437,6	MCF-7	breast:
4	chr1:40505136..40505759-chr2:96808818..96809336,2	Hela-S3	cervix:
5	chr2:96808739..96811929-chr2:96872960..96875920,3	MCF-7	breast:
6	chr2:96808076..96814305-chr2:96871431..96875215,8	MCF-7	breast:
7	chr14:90862942..90863444-chr2:96808676..96809600,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000222040	Chromatin interaction
ENSG00000144021	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000198668	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000135956	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2969489	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs749457	0.84[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1840487	chr2:96582807-96836512	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874672	chr2:96637870-96809331	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv874673	chr2:96647856-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv1825266	chr2:96704118-96830753	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv1004129	chr2:96738585-96825363	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
7	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
8	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
9	nsv874675	chr2:96741944-96825363	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv874676	chr2:96753149-96825363	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	esv1819594	chr2:96755038-96833480	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv1008495	chr2:96755070-96825363	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
13	nsv1002392	chr2:96756289-96815149	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
14	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
15	nsv1004977	chr2:96757107-96819188	Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
16	nsv1015000	chr2:96757107-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
17	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
18	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
19	nsv1007132	chr2:96767204-96829489	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1724120	ADRA2B	cis	cerebellum	SCAN
rs1724120	KIAA1310	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96798000-96809400	Weak transcription	Gastric	stomach
2	chr2:96802600-96810200	Weak transcription	HSMMtube	muscle
3	chr2:96804800-96809400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:96804800-96809600	Weak transcription	Pancreas	Pancrea
5	chr2:96805000-96809600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:96805200-96809400	Weak transcription	Stomach Mucosa	stomach
7	chr2:96805200-96809800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:96805400-96809600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:96805400-96809600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr2:96806800-96810800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
11	chr2:96806800-96810800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:96807600-96809600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:96807800-96809600	Enhancers	Esophagus	oesophagus
14	chr2:96807800-96810400	Transcr. at gene 5' and 3'	Thymus	Thymus
15	chr2:96808000-96809400	Genic enhancers	Spleen	Spleen
16	chr2:96808000-96809800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr2:96808000-96810000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:96808000-96810200	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
19	chr2:96808000-96810200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
20	chr2:96808000-96810400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
21	chr2:96808200-96809600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:96808200-96809600	Strong transcription	Fetal Stomach	stomach
23	chr2:96808200-96809800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
24	chr2:96808200-96809800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr2:96808200-96810000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
26	chr2:96808400-96809800	Enhancers	Fetal Muscle Leg	muscle
27	chr2:96808400-96810000	Transcr. at gene 5' and 3'	Hela-S3	cervix
28	chr2:96808400-96810200	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:96808400-96810400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
30	chr2:96808600-96809400	Enhancers	Colonic Mucosa	Colon
31	chr2:96808600-96809800	Enhancers	Primary B cells from peripheral blood	blood
32	chr2:96808600-96809800	Active TSS	Monocytes-CD14+_RO01746	blood
33	chr2:96808600-96810000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
34	chr2:96808600-96810400	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:96808800-96809400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr2:96808800-96809600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr2:96808800-96809800	Strong transcription	Fetal Intestine Small	intestine
38	chr2:96808800-96809800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:96808800-96810000	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr2:96808800-96811800	Weak transcription	K562	blood
41	chr2:96809000-96809400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr2:96809000-96809400	Active TSS	Osteobl	bone
43	chr2:96809000-96809600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:96809000-96809600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr2:96809000-96810000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:96809000-96810200	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
47	chr2:96809000-96810200	Enhancers	Brain Hippocampus Middle	brain
48	chr2:96809200-96809400	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr2:96809200-96809600	Genic enhancers	Primary hematopoietic stem cells	blood
50	chr2:96809200-96809600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links