Variant report

Variant	rs2249256
Chromosome Location	chr8:104136997-104136998
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:104135020..104140740-chr8:104310050..104312668,5	MCF-7	breast:
2	chr8:104136959..104137770-chr8:104277035..104277881,4	MCF-7	breast:
3	chr8:104135980..104138814-chr8:104426919..104429074,2	MCF-7	breast:
4	chr8:104136846..104137840-chr8:104219113..104220225,5	MCF-7	breast:
5	chr8:104123501..104124311-chr8:104136953..104137651,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247081	Chromatin interaction
ENSG00000164930	Chromatin interaction
ENSG00000164933	Chromatin interaction
ENSG00000164934	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1113126	0.93[ASN][1000 genomes]
rs12056711	0.83[JPT][hapmap]
rs13259545	0.83[JPT][hapmap]
rs13264626	0.83[JPT][hapmap]
rs13274504	0.81[ASN][1000 genomes]
rs1497449	0.89[ASN][1000 genomes]
rs1497450	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1497451	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1497452	0.91[ASN][1000 genomes]
rs1846063	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1846064	0.91[ASN][1000 genomes]
rs1976326	0.99[ASN][1000 genomes]
rs2132867	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2249240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2249254	0.90[ASN][1000 genomes]
rs2249255	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap]
rs2256164	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2454000	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2454001	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2454002	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2454003	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2454004	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2454005	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2454006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2454013	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2454014	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2454032	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2454033	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2454036	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2454037	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2454038	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2515175	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2515176	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2515178	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2515181	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2515182	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2515184	0.91[ASN][1000 genomes]
rs2515185	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2515186	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.91[ASN][1000 genomes]
rs2515190	0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2935579	0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2935593	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3019158	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3019159	0.86[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4734071	0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4734687	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4734689	0.89[ASN][1000 genomes]
rs4734690	0.89[ASN][1000 genomes]
rs61274078	0.80[ASN][1000 genomes]
rs7001897	0.89[ASN][1000 genomes]
rs7014418	0.86[ASN][1000 genomes]
rs72507596	0.80[ASN][1000 genomes]
rs953253	0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs991312	0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2249256	SLC25A32	cis	cerebellum	SCAN
rs2249256	BAALC	cis	parietal	SCAN
rs2249256	BAALC	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104132200-104139600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr8:104132800-104137000	Weak transcription	Brain Substantia Nigra	brain
3	chr8:104132800-104137200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr8:104133000-104137000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr8:104133200-104137000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr8:104133200-104137000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr8:104133200-104137200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr8:104133200-104137400	Weak transcription	Brain Angular Gyrus	brain
9	chr8:104133400-104137000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr8:104133400-104137200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr8:104134200-104137000	Weak transcription	Brain Anterior Caudate	brain
12	chr8:104134400-104145000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr8:104134600-104137400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr8:104134800-104137400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr8:104135400-104137200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr8:104135600-104137000	Weak transcription	NHDF-Ad	bronchial
17	chr8:104135600-104137200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr8:104135600-104137200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr8:104135600-104137400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr8:104135600-104139400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr8:104135800-104137000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr8:104135800-104137000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr8:104135800-104137200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr8:104135800-104137200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr8:104135800-104137200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr8:104135800-104139400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr8:104135800-104139400	Weak transcription	Osteobl	bone
28	chr8:104136000-104137000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr8:104136000-104143200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr8:104136400-104137000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr8:104136800-104137200	Enhancers	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links