Variant report

Variant	rs1257021
Chromosome Location	chr2:97615423-97615424
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97533737..97536220-chr2:97612669..97617368,4	K562	blood:
2	chr2:97530625..97533961-chr2:97614118..97617148,3	K562	blood:
3	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
4	chr2:97562462..97564886-chr2:97613357..97616382,3	MCF-7	breast:
5	chr2:97521500..97526453-chr2:97614513..97620136,8	K562	blood:
6	chr2:97521500..97526547-chr2:97614513..97619168,8	K562	blood:
7	chr2:97612710..97615521-chr2:97617240..97619718,4	K562	blood:

Variant related genes	Relation type
ENSG00000168758	Chromatin interaction
ENSG00000213337	Chromatin interaction
ENSG00000163126	Chromatin interaction
ENSG00000168754	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10874468	0.81[CHB][hapmap]
rs11164113	0.88[CHB][hapmap];0.84[AMR][1000 genomes]
rs1148592	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1148595	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs11676858	0.88[CHB][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs11680224	0.87[CHB][hapmap];0.84[AMR][1000 genomes]
rs11688134	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1257006	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1257010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1257013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1257014	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1257022	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1257026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1257084	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1257089	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1257101	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1257117	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12995874	0.80[ASN][1000 genomes]
rs12997297	0.86[AMR][1000 genomes]
rs13009659	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1669760	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1796025	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1796043	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1796048	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1796050	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2463904	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4063952	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6730782	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7569432	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs9324210	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1257021	UNQ2430	cis	multi-tissue	Pritchard

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97606200-97616000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:97610400-97616600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:97610400-97617400	Enhancers	Brain Substantia Nigra	brain
4	chr2:97611000-97615600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:97611000-97616400	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr2:97611000-97616600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:97611200-97615800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:97611200-97616000	Weak transcription	Fetal Thymus	thymus
9	chr2:97611200-97616200	Weak transcription	Brain Germinal Matrix	brain
10	chr2:97611200-97616400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr2:97611200-97616400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr2:97611200-97616800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:97611200-97618000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:97611400-97615600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:97611400-97615600	Weak transcription	Fetal Brain Male	brain
16	chr2:97611400-97615800	Weak transcription	Fetal Lung	lung
17	chr2:97611400-97616000	Weak transcription	Fetal Brain Female	brain
18	chr2:97611400-97616000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:97611600-97616000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:97611800-97615800	Weak transcription	Fetal Heart	heart
21	chr2:97612400-97615600	Enhancers	Brain Hippocampus Middle	brain
22	chr2:97612800-97620200	Enhancers	K562	blood
23	chr2:97613000-97615600	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr2:97613200-97616600	Enhancers	Brain Angular Gyrus	brain
25	chr2:97613200-97617400	Enhancers	Brain Anterior Caudate	brain
26	chr2:97614200-97616600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:97614600-97616600	Weak transcription	Esophagus	oesophagus
28	chr2:97614800-97619800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr2:97615200-97618200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:97615400-97615600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:97615400-97615800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr2:97615400-97616000	Enhancers	Colon Smooth Muscle	Colon
33	chr2:97615400-97617200	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr2:97615400-97617400	Bivalent Enhancer	Fetal Stomach	stomach
35	chr2:97615400-97621800	Enhancers	Colonic Mucosa	Colon

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