Variant report

Variant	rs2556406
Chromosome Location	chr2:49587323-49587324
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:49586512..49588631-chr2:49595229..49597558,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12471870	1.00[ASN][1000 genomes]
rs17038708	1.00[ASN][1000 genomes]
rs62162813	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs817017	1.00[ASN][1000 genomes]
rs817071	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs817075	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs817076	1.00[ASN][1000 genomes]
rs817081	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993555	chr2:49299168-49781707	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv869321	chr2:49316909-49587401	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1005336	chr2:49422587-49737964	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv535686	chr2:49422587-49737964	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1006675	chr2:49422587-49737965	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535687	chr2:49422587-49737965	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv998367	chr2:49441886-49795482	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv874013	chr2:49498006-49690836	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv874014	chr2:49510173-49668973	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv581799	chr2:49519335-49660335	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv581807	chr2:49533498-49660335	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv998662	chr2:49535756-49724779	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1014952	chr2:49538537-49766680	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv535688	chr2:49538537-49766680	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv999028	chr2:49545029-49661323	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv581823	chr2:49565575-49650145	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv1002863	chr2:49575829-49650145	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv581824	chr2:49580566-49635681	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv1012441	chr2:49581384-49804591	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv535689	chr2:49581384-49804591	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2556406	LOC388946	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:49583400-49587600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr2:49586400-49587800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr2:49586400-49588000	Enhancers	Fetal Brain Male	brain
4	chr2:49586600-49587600	Enhancers	Fetal Brain Female	brain
5	chr2:49586600-49588000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr2:49586600-49588800	Enhancers	Brain Germinal Matrix	brain
7	chr2:49587000-49587400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr2:49587000-49587800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:49587000-49588000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr2:49587000-49588000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr2:49587200-49587800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr2:49587200-49588000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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