Variant report

Variant	rs10861171
Chromosome Location	chr12:104617778-104617779
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr12:104617653-104617923	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104609968..104613463-chr12:104614519..104618118,3	K562	blood:
2	chr12:104617645..104619997-chr12:104678987..104680569,2	K562	blood:
3	chr12:104617675..104620122-chr12:104673280..104676243,2	K562	blood:
4	chr12:104611527..104621556-chr12:104677756..104684608,20	MCF-7	breast:

Variant related genes	Relation type
TXNRD1	TF binding region
ENSG00000257732	Chromatin interaction
ENSG00000198431	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10745993	0.83[AFR][1000 genomes]
rs10861169	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs10861170	0.92[AFR][1000 genomes]
rs11111940	0.84[YRI][hapmap]
rs11836627	0.82[CHB][hapmap]
rs12320159	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321026	0.85[AFR][1000 genomes]
rs4475991	0.91[LWK][hapmap];0.91[MKK][hapmap]
rs4964256	0.83[AFR][1000 genomes]
rs4964678	0.85[AFR][1000 genomes]
rs60903309	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539130	0.83[AFR][1000 genomes]
rs7296260	0.84[EUR][1000 genomes]
rs7297296	0.83[AFR][1000 genomes]
rs7297956	0.84[YRI][hapmap]
rs7313063	0.82[ASW][hapmap];0.91[LWK][hapmap];0.85[MKK][hapmap];0.81[YRI][hapmap]
rs73392585	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394503	1.00[ASN][1000 genomes]
rs7958262	0.96[YRI][hapmap]
rs7966970	0.85[AFR][1000 genomes]
rs7975524	0.96[YRI][hapmap];0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
2	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers 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	32 gene(s)	inside rSNPs	diseases
6	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10861171	DRAM1	cis	cerebellum	SCAN
rs10861171	SLC5A8	cis	parietal	SCAN
rs10861171	UHRF1BP1L	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104614000-104619600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr12:104614000-104623400	Weak transcription	Right Atrium	heart
3	chr12:104614200-104619800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:104615000-104620200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:104615000-104625800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:104616600-104618000	Enhancers	Fetal Lung	lung
7	chr12:104616800-104617800	Flanking Active TSS	A549	lung
8	chr12:104616800-104617800	Enhancers	NHLF	lung
9	chr12:104617000-104617800	Enhancers	Stomach Mucosa	stomach
10	chr12:104617200-104618000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:104617400-104617800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr12:104617400-104617800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:104617400-104617800	Enhancers	Duodenum Mucosa	Duodenum
14	chr12:104617400-104617800	Enhancers	Hela-S3	cervix
15	chr12:104617400-104617800	Enhancers	HSMMtube	muscle
16	chr12:104617400-104618000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr12:104617400-104618000	Enhancers	Fetal Stomach	stomach
18	chr12:104617400-104618000	Enhancers	GM12878-XiMat	blood
19	chr12:104617400-104618000	Enhancers	HMEC	breast
20	chr12:104617400-104618800	Enhancers	Placenta	Placenta
21	chr12:104617400-104619400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr12:104617600-104617800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain

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