Variant report

Variant	rs2812316
Chromosome Location	chr9:108165651-108165652
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:108153124..108158591-chr9:108160157..108165830,7	MCF-7	breast:
2	chr9:108006964..108008816-chr9:108165166..108168105,2	MCF-7	breast:
3	chr9:108154477..108157251-chr9:108163904..108166512,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10491810	1.00[ASN][1000 genomes]
rs10991639	1.00[ASN][1000 genomes]
rs12339823	1.00[ASN][1000 genomes]
rs12340765	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12342542	1.00[ASN][1000 genomes]
rs12344130	1.00[ASN][1000 genomes]
rs13294525	1.00[ASN][1000 genomes]
rs13294539	1.00[ASN][1000 genomes]
rs1410837	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410839	1.00[ASN][1000 genomes]
rs1553870	1.00[ASN][1000 genomes]
rs1553873	1.00[ASN][1000 genomes]
rs16924529	1.00[ASN][1000 genomes]
rs16924530	1.00[ASN][1000 genomes]
rs17246524	1.00[ASN][1000 genomes]
rs17305886	1.00[ASN][1000 genomes]
rs17305963	1.00[ASN][1000 genomes]
rs2771031	1.00[ASN][1000 genomes]
rs2771033	1.00[ASN][1000 genomes]
rs2771040	1.00[ASN][1000 genomes]
rs2812314	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3199966	1.00[ASN][1000 genomes]
rs35603631	1.00[ASN][1000 genomes]
rs41296093	1.00[ASN][1000 genomes]
rs6479311	1.00[ASN][1000 genomes]
rs7024985	1.00[ASN][1000 genomes]
rs7045091	1.00[ASN][1000 genomes]
rs724069	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858401	1.00[ASN][1000 genomes]
rs907230	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2812316	SLC44A1	Cis_1M	lymphoblastoid	RTeQTL
rs2812316	LRRC40	trans	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108125000-108166800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:108146800-108177600	Weak transcription	Left Ventricle	heart
3	chr9:108148400-108168000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:108152600-108166000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:108155400-108172600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr9:108156800-108165800	Weak transcription	Fetal Brain Male	brain
7	chr9:108159800-108166000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:108160000-108165800	Weak transcription	Brain Angular Gyrus	brain
9	chr9:108163200-108166000	Enhancers	H9 Cell Line	embryonic stem cell
10	chr9:108163200-108166000	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr9:108163200-108168400	Enhancers	H1 Cell Line	embryonic stem cell
12	chr9:108163800-108167400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:108164000-108165800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr9:108164200-108166400	Enhancers	Brain Hippocampus Middle	brain
15	chr9:108164200-108167200	Enhancers	Brain Substantia Nigra	brain
16	chr9:108164400-108165800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:108164400-108165800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr9:108164400-108167800	Weak transcription	Fetal Heart	heart
19	chr9:108164600-108167800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:108165200-108165800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr9:108165200-108166400	Enhancers	Brain Cingulate Gyrus	brain
22	chr9:108165400-108165800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr9:108165400-108167800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr9:108165600-108165800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
25	chr9:108165600-108166000	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr9:108165600-108166000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr9:108165600-108166200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr9:108165600-108166200	Enhancers	Brain Anterior Caudate	brain
29	chr9:108165600-108166400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:108165600-108166600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr9:108165600-108166800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:108165600-108167200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr9:108165600-108170000	Enhancers	Dnd41	blood

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