Variant report

Variant	rs1229578
Chromosome Location	chr10:93851714-93851715
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	chr10:93838081..93839704-chr10:93849974..93852116,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10786029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10786031	0.80[ASN][1000 genomes]
rs10786033	0.80[ASN][1000 genomes]
rs10882028	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10882042	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1099379	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1229579	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1622656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1711849	0.95[ASN][1000 genomes]
rs1776209	1.00[YRI][hapmap]
rs2767654	0.87[ASN][1000 genomes]
rs3781229	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3824734	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs4642988	0.86[ASN][1000 genomes]
rs4933227	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4933228	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6583804	0.86[ASN][1000 genomes]
rs701844	0.91[ASN][1000 genomes]
rs701846	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7078559	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7087501	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7090737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7091853	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7897555	0.80[ASN][1000 genomes]
rs7919840	0.84[ASN][1000 genomes]
rs7920520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs833385	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs855697	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs855698	0.92[ASN][1000 genomes]
rs855699	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs855702	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs855703	0.92[ASN][1000 genomes]
rs855704	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs855706	0.85[ASN][1000 genomes]
rs855707	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs855708	0.94[ASN][1000 genomes]
rs855710	0.92[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	nsv1051226	chr10:93711296-93915586	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv540745	chr10:93711296-93915586	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1042818	chr10:93715483-93855032	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv895893	chr10:93747260-93875264	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv975763	chr10:93822289-94105956	Enhancers Bivalent Enhancer Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1229578	TNKS2	cis	parietal	SCAN
rs1229578	PIPSL	cis	cerebellum	SCAN
rs1229578	RNLS	cis	parietal	SCAN
rs1229578	LIPM	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93836000-93853200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr10:93841200-93853800	Weak transcription	Pancreas	Pancrea
3	chr10:93841200-93872400	Weak transcription	Spleen	Spleen
4	chr10:93841200-93881600	Weak transcription	Esophagus	oesophagus
5	chr10:93844000-93860800	Weak transcription	Psoas Muscle	Psoas
6	chr10:93845800-93856400	Weak transcription	Left Ventricle	heart
7	chr10:93847800-93861000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr10:93848000-93851800	Weak transcription	Fetal Intestine Small	intestine
9	chr10:93848200-93860800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr10:93848800-93856200	Weak transcription	Liver	Liver
11	chr10:93850600-93851800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr10:93851000-93851800	Enhancers	Brain Anterior Caudate	brain
13	chr10:93851000-93852200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr10:93851000-93852200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr10:93851000-93852400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr10:93851200-93852000	Enhancers	Brain Hippocampus Middle	brain
17	chr10:93851200-93852200	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr10:93851200-93852400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr10:93851200-93853400	Enhancers	GM12878-XiMat	blood
20	chr10:93851400-93851800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr10:93851400-93852000	Enhancers	HUES6 Cell Line	embryonic stem cell

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