Variant report

Variant	rs11897706
Chromosome Location	chr2:100558451-100558452
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	chr2:100435277..100437585-chr2:100558410..100560429,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10165066	0.97[EUR][1000 genomes]
rs10183465	0.96[EUR][1000 genomes]
rs10187195	0.96[EUR][1000 genomes]
rs10189707	0.97[EUR][1000 genomes]
rs10198187	0.96[EUR][1000 genomes]
rs10209198	0.86[EUR][1000 genomes]
rs10211423	1.00[MEX][hapmap]
rs11887136	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13382597	0.95[EUR][1000 genomes]
rs13383014	0.96[EUR][1000 genomes]
rs13385193	0.83[EUR][1000 genomes]
rs13393937	0.89[EUR][1000 genomes]
rs13405987	0.95[EUR][1000 genomes]
rs13410695	0.96[EUR][1000 genomes]
rs13410884	0.92[EUR][1000 genomes]
rs13413309	0.93[EUR][1000 genomes]
rs13416574	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1574207	0.82[EUR][1000 genomes]
rs17023362	0.83[EUR][1000 genomes]
rs17023378	0.83[EUR][1000 genomes]
rs17023391	0.82[EUR][1000 genomes]
rs17023393	0.82[EUR][1000 genomes]
rs17436955	0.84[EUR][1000 genomes]
rs2001722	0.82[EUR][1000 genomes]
rs2309775	0.83[EUR][1000 genomes]
rs4129805	0.95[EUR][1000 genomes]
rs4449188	0.86[EUR][1000 genomes]
rs4641993	1.00[EUR][1000 genomes]
rs55649403	0.81[EUR][1000 genomes]
rs55681051	0.81[EUR][1000 genomes]
rs56332326	0.97[EUR][1000 genomes]
rs57360658	0.99[EUR][1000 genomes]
rs58270548	0.86[EUR][1000 genomes]
rs62147652	0.88[EUR][1000 genomes]
rs62147658	0.88[EUR][1000 genomes]
rs62147659	0.86[EUR][1000 genomes]
rs62149260	0.86[EUR][1000 genomes]
rs62149262	0.86[EUR][1000 genomes]
rs62149263	0.86[EUR][1000 genomes]
rs62149268	0.86[EUR][1000 genomes]
rs62149270	0.85[EUR][1000 genomes]
rs62149271	0.95[EUR][1000 genomes]
rs62149272	0.85[EUR][1000 genomes]
rs62149296	0.95[EUR][1000 genomes]
rs62149297	0.85[EUR][1000 genomes]
rs62149298	0.84[EUR][1000 genomes]
rs62149299	0.84[EUR][1000 genomes]
rs62149301	0.84[EUR][1000 genomes]
rs62149302	0.95[EUR][1000 genomes]
rs6736239	0.81[EUR][1000 genomes]
rs72819146	0.88[EUR][1000 genomes]
rs72819147	0.97[EUR][1000 genomes]
rs72819148	0.86[EUR][1000 genomes]
rs72819149	0.86[EUR][1000 genomes]
rs72819157	0.96[EUR][1000 genomes]
rs72819165	0.81[EUR][1000 genomes]
rs7425132	0.99[EUR][1000 genomes]
rs7573669	0.88[EUR][1000 genomes]
rs7576469	0.96[EUR][1000 genomes]
rs7577040	0.99[EUR][1000 genomes]
rs9308831	0.84[EUR][1000 genomes]
rs9308832	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1003114	chr2:100480432-100601586	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11897706	AFF3	cis	parietal	SCAN
rs11897706	CREG2	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100540200-100572600	Weak transcription	Adipose Nuclei	Adipose
2	chr2:100541800-100575000	Weak transcription	Brain Germinal Matrix	brain
3	chr2:100545600-100572600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr2:100546000-100559400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:100547600-100569200	Weak transcription	Fetal Stomach	stomach
6	chr2:100547600-100577200	Weak transcription	Thymus	Thymus
7	chr2:100549000-100562200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:100550800-100562200	Strong transcription	Primary B cells from cord blood	blood
9	chr2:100550800-100577000	Weak transcription	Spleen	Spleen
10	chr2:100550800-100618200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:100551200-100563200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:100551400-100563600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:100553400-100569800	Weak transcription	Lung	lung
14	chr2:100553600-100573200	Strong transcription	Primary B cells from peripheral blood	blood
15	chr2:100553600-100573400	Weak transcription	Fetal Brain Female	brain
16	chr2:100554600-100558600	Strong transcription	Primary hematopoietic stem cells	blood
17	chr2:100555000-100566000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:100556600-100560000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:100557200-100559000	Enhancers	NH-A	brain
20	chr2:100557200-100562600	Enhancers	Fetal Heart	heart
21	chr2:100557400-100558800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:100557600-100558800	Strong transcription	Primary T cells from cord blood	blood
23	chr2:100557600-100559600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:100557600-100560600	Weak transcription	Gastric	stomach
25	chr2:100557600-100560600	Weak transcription	Left Ventricle	heart
26	chr2:100557600-100564200	Weak transcription	Ovary	ovary
27	chr2:100557800-100559200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:100558200-100558800	ZNF genes & repeats	Fetal Lung	lung
29	chr2:100558200-100559200	Weak transcription	Liver	Liver
30	chr2:100558400-100558800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:100558400-100559600	Weak transcription	Osteobl	bone
32	chr2:100558400-100564400	Weak transcription	Dnd41	blood

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