Variant report

Variant	rs1402127
Chromosome Location	chr2:50624755-50624756
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:50621939..50623486-chr2:50624372..50627015,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10182151	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10191436	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap]
rs10194754	0.85[ASN][1000 genomes]
rs11125300	0.82[CEU][hapmap]
rs11125301	0.82[CEU][hapmap]
rs12465806	0.82[CEU][hapmap]
rs12622261	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13382330	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs13394447	0.80[CEU][hapmap]
rs1402122	0.83[CEU][hapmap]
rs1402126	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs1402129	0.82[CEU][hapmap]
rs1520450	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs1520453	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1818713	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs1829534	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs1851013	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs1915174	0.82[CEU][hapmap]
rs1949569	0.82[CEU][hapmap]
rs2037387	0.82[CEU][hapmap]
rs2351518	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2351519	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4318425	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4971669	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4971671	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs4971673	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722443	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7559624	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7574552	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7577661	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7587241	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7599863	0.83[EUR][1000 genomes]
rs939400	0.85[CHB][hapmap]
rs939401	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs9678669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv932915	chr2:50306630-50628415	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1000653	chr2:50417660-51083470	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv535693	chr2:50417660-51083470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv948548	chr2:50569117-50695100	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv948361	chr2:50611076-50785178	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1402127	ARHGAP26	cis	Frontal Cortex	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50622600-50626000	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr2:50623200-50625200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr2:50623200-50625800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:50623600-50625200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr2:50624200-50624800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:50624400-50626000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr2:50624400-50626200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr2:50624400-50628600	Weak transcription	Stomach Mucosa	stomach
9	chr2:50624400-50629200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:50624600-50625800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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