Variant report

Variant	rs16870228
Chromosome Location	chr8:104191982-104191983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:104187136..104189452-chr8:104190245..104193206,2	K562	blood:
2	chr8:104190126..104192266-chr8:104202856..104205626,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1000460	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1000461	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10102706	0.85[ASN][1000 genomes]
rs12543973	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13275933	0.88[ASN][1000 genomes]
rs1494271	0.89[AMR][1000 genomes]
rs1494272	0.93[ASN][1000 genomes]
rs1494273	0.85[ASN][1000 genomes]
rs16870210	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs16870221	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16870229	0.87[AMR][1000 genomes]
rs1826642	0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes]
rs36016728	0.90[AMR][1000 genomes]
rs3956319	0.89[AMR][1000 genomes]
rs59216783	0.84[EUR][1000 genomes]
rs61607037	0.88[ASN][1000 genomes]
rs713369	0.83[AMR][1000 genomes]
rs72673306	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7827695	0.86[ASN][1000 genomes]
rs954782	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs954783	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9693655	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831413	chr8:104085141-104269789	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	esv1848810	chr8:104128496-104369288	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv1844303	chr8:104128696-104369090	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	esv14660	chr8:104182119-104245529	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16870228	BAALC	cis	cerebellum	SCAN
rs16870228	BAALC	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104186400-104195800	Weak transcription	NHLF	lung
2	chr8:104187000-104192000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr8:104187200-104193800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr8:104187400-104192000	Weak transcription	Aorta	Aorta
5	chr8:104187400-104196600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr8:104187800-104192000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr8:104187800-104192000	Weak transcription	Brain Anterior Caudate	brain
8	chr8:104187800-104200800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr8:104188000-104195000	Weak transcription	NHDF-Ad	bronchial
10	chr8:104188000-104196600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr8:104188200-104192200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr8:104188400-104196400	Weak transcription	Osteobl	bone
13	chr8:104188600-104192000	Weak transcription	Brain Hippocampus Middle	brain
14	chr8:104189200-104192200	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr8:104191200-104192800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr8:104191200-104194400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr8:104191400-104192400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr8:104191400-104192400	Enhancers	Brain Substantia Nigra	brain
19	chr8:104191400-104192800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr8:104191400-104193000	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr8:104191400-104193200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr8:104191400-104193200	Enhancers	Brain Angular Gyrus	brain
23	chr8:104191400-104193600	Enhancers	Spleen	Spleen
24	chr8:104191400-104198200	Enhancers	Primary hematopoietic stem cells	blood
25	chr8:104191600-104193000	Enhancers	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links