Variant report

Variant	rs2139417
Chromosome Location	chr2:152887887-152887888
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	chr2:152887207..152889043-chr2:153029547..153032320,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115145	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10190546	0.88[YRI][hapmap]
rs10930888	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10930892	0.89[CEU][hapmap]
rs12471157	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477734	0.84[AMR][1000 genomes]
rs12616521	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12619485	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16830598	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs16830616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1949521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2345160	0.81[CHB][hapmap]
rs2881059	0.94[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35478891	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3845845	1.00[ASW][hapmap];0.90[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4146376	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes]
rs4362556	0.95[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4664075	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4664076	0.87[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.93[YRI][hapmap]
rs4664511	0.84[MEX][hapmap]
rs4664513	0.87[CHB][hapmap]
rs58248711	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58402146	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58761979	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61156093	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6433726	0.87[CHB][hapmap]
rs6433777	0.87[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.80[ASN][1000 genomes]
rs6721518	0.87[CHB][hapmap];0.84[MEX][hapmap]
rs6728019	0.87[CHB][hapmap]
rs6748530	0.81[CHB][hapmap]
rs6755776	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72621651	0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7604835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7607341	0.81[CHB][hapmap]
rs7607695	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9917162	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9917211	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9917218	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv875287	chr2:152714680-153110573	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv875288	chr2:152716628-153183646	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv875289	chr2:152720030-153183646	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv875290	chr2:152803129-152920126	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	esv1847028	chr2:152863856-153045036	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2139417	STAM2	cis	parietal	SCAN
rs2139417	C11orf17	trans	cerebellum	SCAN
rs2139417	TNFAIP6	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152882800-152889600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:152882800-152894200	Weak transcription	Brain Anterior Caudate	brain
3	chr2:152884200-152889600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:152887200-152888600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr2:152887400-152888000	Enhancers	Primary B cells from cord blood	blood
6	chr2:152887400-152888200	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr2:152887400-152888200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:152887400-152888400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:152887400-152888600	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr2:152887400-152888800	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr2:152887600-152888400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:152887600-152888600	Enhancers	Fetal Brain Male	brain
13	chr2:152887800-152888600	Enhancers	GM12878-XiMat	blood
14	chr2:152887800-152889200	Enhancers	Fetal Brain Female	brain

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