Variant report

Variant	rs9854863
Chromosome Location	chr3:121503554-121503555
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121503081..121505086-chr3:121506757..121508419,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs16845505	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60154494	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72626328	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72626329	0.99[ASN][1000 genomes]
rs9818226	0.84[EUR][1000 genomes]
rs9856046	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9861782	0.81[EUR][1000 genomes]
rs9862127	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9863007	0.81[EUR][1000 genomes]
rs9868875	0.84[EUR][1000 genomes]
rs9882312	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9884018	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv877383	chr3:121465220-121650736	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv432483	chr3:121488995-121629634	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv934077	chr3:121491540-121507705	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv932985	chr3:121491698-121507705	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9854863	GOLGB1	cis	multi-tissue	Pritchard
rs9854863	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs9854863	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs9854863	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121486200-121526600	Weak transcription	Stomach Mucosa	stomach
2	chr3:121486800-121532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:121487000-121509000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:121487400-121512200	Strong transcription	Fetal Thymus	thymus
5	chr3:121487400-121512400	Strong transcription	Dnd41	blood
6	chr3:121487800-121509000	Strong transcription	Fetal Intestine Large	intestine
7	chr3:121487800-121516400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:121487800-121519000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr3:121488000-121507200	Weak transcription	Brain Substantia Nigra	brain
10	chr3:121488000-121511000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:121488000-121512200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:121488000-121512600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:121488400-121505600	Weak transcription	Fetal Heart	heart
14	chr3:121488400-121509600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:121488600-121509000	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:121488600-121510200	Strong transcription	Primary B cells from peripheral blood	blood
17	chr3:121488600-121517800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr3:121489000-121509200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr3:121489600-121507000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:121489800-121506200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:121489800-121506400	Weak transcription	Gastric	stomach
22	chr3:121489800-121508000	Weak transcription	Esophagus	oesophagus
23	chr3:121489800-121508800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:121489800-121510600	Weak transcription	Spleen	Spleen
25	chr3:121489800-121514800	Weak transcription	Small Intestine	intestine
26	chr3:121489800-121529800	Weak transcription	Aorta	Aorta
27	chr3:121490000-121529800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:121490000-121529800	Weak transcription	Pancreas	Pancrea
29	chr3:121491600-121506600	Weak transcription	NHDF-Ad	bronchial
30	chr3:121491600-121507000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:121491600-121552600	Weak transcription	NHLF	lung
32	chr3:121494200-121504800	Weak transcription	Brain Germinal Matrix	brain
33	chr3:121494200-121505400	Weak transcription	Colonic Mucosa	Colon
34	chr3:121494200-121509200	Strong transcription	Primary B cells from cord blood	blood
35	chr3:121494200-121510600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:121494200-121544200	Weak transcription	Fetal Brain Male	brain
37	chr3:121494400-121512400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:121494400-121518800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:121494400-121530000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:121494800-121516000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:121496000-121504800	Strong transcription	Hela-S3	cervix
42	chr3:121497000-121504600	Weak transcription	Fetal Intestine Small	intestine
43	chr3:121498000-121509000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:121498000-121510200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr3:121498400-121509200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:121498600-121509000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:121499600-121505600	Weak transcription	HSMMtube	muscle
48	chr3:121500000-121504000	Weak transcription	Ovary	ovary
49	chr3:121500000-121504600	Weak transcription	Lung	lung
50	chr3:121500200-121503600	Weak transcription	Thymus	Thymus

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