Variant report

Variant	rs1796048
Chromosome Location	chr2:97643576-97643577
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11164113	0.85[CHB][hapmap]
rs1148587	0.83[EUR][1000 genomes]
rs1148591	0.81[EUR][1000 genomes]
rs1148592	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1148593	0.82[ASN][1000 genomes]
rs1148594	0.83[EUR][1000 genomes]
rs1148595	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11676858	1.00[ASW][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.89[MKK][hapmap]
rs11680224	0.85[CHB][hapmap]
rs11688134	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11688903	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1257006	0.82[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs1257010	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1257013	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1257014	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1257021	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1257022	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1257026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1257084	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap]
rs1257089	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1257101	0.84[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs1257117	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12995874	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1669760	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1796025	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1796043	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1796050	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2443873	0.93[JPT][hapmap]
rs2463904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4063952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6730782	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs70964893	0.87[AFR][1000 genomes]
rs7566937	0.81[CHB][hapmap]
rs7569432	0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs9324210	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription 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	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription 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 miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv582497	chr2:97569305-97715154	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv2757819	chr2:97571109-98336507	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
11	esv2759077	chr2:97571109-98336507	Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
12	nsv1001432	chr2:97591069-97671395	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	esv32727	chr2:97616488-97643975	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
14	nsv582498	chr2:97639135-97715154	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1796048	ANKRD39	cis	cerebellum	SCAN
rs1796048	ACTR1B	cis	cerebellum	SCAN
rs1796048	ANKRD36B	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97620800-97643600	Weak transcription	Right Atrium	heart
2	chr2:97638400-97647600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:97642200-97644200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:97643000-97644000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr2:97643000-97644000	Enhancers	HMEC	breast
6	chr2:97643200-97643600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr2:97643200-97643600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:97643200-97643600	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr2:97643200-97643600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr2:97643200-97643600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr2:97643200-97643600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:97643200-97643600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:97643200-97643600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
14	chr2:97643200-97643600	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr2:97643200-97643600	Flanking Active TSS	Fetal Kidney	kidney
16	chr2:97643200-97643600	Enhancers	Rectal Smooth Muscle	rectum
17	chr2:97643200-97643600	Flanking Active TSS	A549	lung
18	chr2:97643200-97643600	Flanking Active TSS	HSMMtube	muscle
19	chr2:97643200-97643800	Active TSS	Brain Cingulate Gyrus	brain
20	chr2:97643200-97643800	Active TSS	Brain Hippocampus Middle	brain
21	chr2:97643200-97644000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:97643200-97644000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr2:97643200-97644000	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr2:97643200-97644000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:97643200-97644000	Enhancers	Placenta Amnion	Placenta Amnion
26	chr2:97643200-97644000	Enhancers	NH-A	brain
27	chr2:97643200-97644200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:97643200-97644200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:97643200-97644200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr2:97643200-97644400	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr2:97643400-97643600	Enhancers	H1 Cell Line	embryonic stem cell
32	chr2:97643400-97643600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:97643400-97643600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr2:97643400-97643600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:97643400-97643600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:97643400-97643600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:97643400-97643600	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr2:97643400-97643600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:97643400-97643600	Flanking Active TSS	Brain Substantia Nigra	brain
40	chr2:97643400-97643600	Enhancers	Colon Smooth Muscle	Colon
41	chr2:97643400-97643600	Enhancers	Duodenum Mucosa	Duodenum
42	chr2:97643400-97643600	Flanking Active TSS	Fetal Lung	lung
43	chr2:97643400-97643600	Enhancers	Fetal Thymus	thymus
44	chr2:97643400-97643600	Flanking Active TSS	Stomach Smooth Muscle	stomach
45	chr2:97643400-97643600	Flanking Active TSS	K562	blood
46	chr2:97643400-97643600	Flanking Active TSS	NHDF-Ad	bronchial
47	chr2:97643400-97643600	Enhancers	NHEK	skin
48	chr2:97643400-97643600	Flanking Active TSS	Osteobl	bone
49	chr2:97643400-97643800	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr2:97643400-97643800	Enhancers	Primary T cells from cord blood	blood

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