Variant report

Variant	rs12992413
Chromosome Location	chr2:97277489-97277490
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97275906..97278636-chr2:97295699..97298377,2	K562	blood:
2	chr2:97274923..97277502-chr2:97277680..97279204,2	K562	blood:
3	chr2:97275865..97277715-chr2:97285589..97288319,2	K562	blood:
4	chr2:97275521..97278497-chr2:97303256..97305741,2	K562	blood:

Variant related genes	Relation type
ENSG00000114982	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1011040	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10184209	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10194468	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12329128	0.96[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12477963	0.87[TSI][hapmap]
rs12717781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12717782	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13007343	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13019986	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13029764	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17685664	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17685766	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2314109	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2579502	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2579505	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs2708976	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2708977	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708978	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34029026	0.91[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs749027	0.86[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv999871	chr2:97157196-97407711	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv535829	chr2:97157196-97407711	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS 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	35 gene(s)	inside rSNPs	diseases
11	nsv469775	chr2:97240926-97412491	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv482586	chr2:97240926-97412491	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv834306	chr2:97241115-97412938	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12992413	ADRA2B	cis	cerebellum	SCAN
rs12992413	LOC285033	cis	parietal	SCAN
rs12992413	FAM178B	cis	parietal	SCAN
rs12992413	TMEM127	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97248400-97283600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:97256200-97282400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:97256600-97283800	Strong transcription	Placenta	Placenta
4	chr2:97256600-97287000	Strong transcription	Dnd41	blood
5	chr2:97257000-97279600	Strong transcription	Fetal Lung	lung
6	chr2:97257400-97279600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr2:97257400-97279600	Strong transcription	Primary hematopoietic stem cells	blood
8	chr2:97257400-97279600	Strong transcription	Duodenum Smooth Muscle	Duodenum
9	chr2:97257400-97279800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:97257400-97279800	Strong transcription	Stomach Smooth Muscle	stomach
11	chr2:97257400-97280000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:97257400-97280800	Strong transcription	Fetal Muscle Leg	muscle
13	chr2:97257400-97282400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr2:97257600-97280800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:97257600-97286400	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:97257800-97279400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:97257800-97279400	Strong transcription	Brain Germinal Matrix	brain
18	chr2:97257800-97279600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr2:97257800-97286800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:97258000-97279400	Strong transcription	Ovary	ovary
21	chr2:97258000-97279400	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:97258000-97283200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr2:97258200-97283200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:97258200-97286400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:97258200-97302800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr2:97258600-97279800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr2:97258800-97279600	Strong transcription	NHLF	lung
28	chr2:97258800-97280000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:97261200-97279600	Strong transcription	Primary T cells from cord blood	blood
30	chr2:97261200-97281000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:97261200-97301600	Strong transcription	Fetal Thymus	thymus
32	chr2:97261400-97279800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:97261400-97282400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:97261600-97283000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:97262200-97280600	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr2:97263600-97279800	Strong transcription	Fetal Brain Female	brain
37	chr2:97263600-97279800	Strong transcription	Fetal Kidney	kidney
38	chr2:97263800-97279600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:97264800-97279600	Strong transcription	Rectal Smooth Muscle	rectum
40	chr2:97265200-97282600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:97265600-97279000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr2:97265600-97279400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:97265600-97280400	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr2:97265800-97280400	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:97266200-97279400	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr2:97266200-97279400	Strong transcription	Esophagus	oesophagus
47	chr2:97266200-97279600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr2:97266200-97279600	Strong transcription	Brain Cingulate Gyrus	brain
49	chr2:97266200-97280600	Strong transcription	Thymus	Thymus
50	chr2:97266200-97287600	Strong transcription	Fetal Muscle Trunk	muscle

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