Variant report

Variant	rs13417566
Chromosome Location	chr2:111592606-111592607
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	chr2:111589730..111592608-chr2:111607480..111611247,3	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10048703	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs10048706	0.88[CEU][hapmap]
rs12463442	0.96[CEU][hapmap];0.99[EUR][1000 genomes]
rs12463526	0.96[CEU][hapmap];0.99[EUR][1000 genomes]
rs13397695	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1543107	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2175824	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2612696	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4494791	0.81[CEU][hapmap]
rs4849105	0.92[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs6730627	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs952249	0.80[CEU][hapmap]

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	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1008758	chr2:111415136-111626467	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv535890	chr2:111415136-111626467	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv997829	chr2:111486961-111780537	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13417566	POLR1B	cis	parietal	SCAN
rs13417566	SULT1C2	cis	cerebellum	SCAN
rs13417566	MALL	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111562800-111604000	Weak transcription	Lung	lung
2	chr2:111590600-111596800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:111590800-111593800	Enhancers	GM12878-XiMat	blood
4	chr2:111590800-111594000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr2:111590800-111594800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:111590800-111596400	Enhancers	H1 Cell Line	embryonic stem cell
7	chr2:111591200-111592800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr2:111591400-111597000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:111591600-111597400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:111591800-111593200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr2:111591800-111594000	Enhancers	H9 Cell Line	embryonic stem cell
12	chr2:111592000-111593200	Enhancers	Primary T cells from cord blood	blood
13	chr2:111592000-111593200	Enhancers	Thymus	Thymus
14	chr2:111592000-111598400	Enhancers	Fetal Thymus	thymus
15	chr2:111592200-111593200	Enhancers	Dnd41	blood
16	chr2:111592200-111595600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:111592400-111593000	Weak transcription	Pancreas	Pancrea
18	chr2:111592400-111593200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr2:111592400-111594600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:111592400-111595600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr2:111592400-111595600	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr2:111592400-111595600	Enhancers	Fetal Brain Male	brain
23	chr2:111592400-111596600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr2:111592400-111596800	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr2:111592400-111597200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr2:111592600-111596200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:111592600-111596200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:111592600-111596200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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