Variant report

Variant	rs9856338
Chromosome Location	chr3:100322043-100322044
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100321992..100322818-chr3:100353419..100354308,2	MCF-7	breast:
2	chr3:100321003..100323549-chr3:100347554..100350487,3	MCF-7	breast:
3	chr3:100181722..100182327-chr3:100321776..100322610,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10428254	0.91[ASN][1000 genomes]
rs10511187	0.92[ASN][1000 genomes]
rs10511188	0.92[ASN][1000 genomes]
rs10936264	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936276	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs1165521	0.86[ASN][1000 genomes]
rs11923487	0.80[ASN][1000 genomes]
rs12634935	0.92[ASN][1000 genomes]
rs12635503	0.92[ASN][1000 genomes]
rs12636790	0.92[ASN][1000 genomes]
rs12637319	0.92[ASN][1000 genomes]
rs1305373	0.92[ASN][1000 genomes]
rs1305375	0.92[ASN][1000 genomes]
rs13069547	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13321761	0.92[ASN][1000 genomes]
rs1471375	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs1520650	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs1531772	0.91[CHB][hapmap];0.92[JPT][hapmap]
rs1676340	0.94[CHB][hapmap];0.91[CHD][hapmap];0.83[JPT][hapmap];0.83[TSI][hapmap]
rs16842463	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs1718275	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs1842732	0.90[ASN][1000 genomes]
rs2169554	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2460719	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4129205	0.81[CEU][hapmap];0.83[CHB][hapmap];0.80[ASN][1000 genomes]
rs57404153	0.80[ASN][1000 genomes]
rs58618663	0.82[ASN][1000 genomes]
rs60151360	0.91[ASN][1000 genomes]
rs61549238	0.84[ASN][1000 genomes]
rs619149	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs653530	0.92[ASN][1000 genomes]
rs661266	0.92[ASN][1000 genomes]
rs6763638	0.81[CEU][hapmap];0.81[CHD][hapmap];0.80[ASN][1000 genomes]
rs6768258	0.92[ASN][1000 genomes]
rs6770693	0.92[ASN][1000 genomes]
rs6771421	0.92[ASN][1000 genomes]
rs6773148	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6783630	0.92[ASN][1000 genomes]
rs6785969	0.92[ASN][1000 genomes]
rs6786853	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73141183	0.85[ASN][1000 genomes]
rs7426414	0.87[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs7426462	0.80[ASN][1000 genomes]
rs7427360	0.80[ASN][1000 genomes]
rs7429915	0.81[CEU][hapmap];0.81[CHD][hapmap];0.92[MEX][hapmap]
rs7432710	0.80[ASN][1000 genomes]
rs7433875	0.80[ASN][1000 genomes]
rs7617909	0.80[ASN][1000 genomes]
rs900235	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs9290097	0.91[ASN][1000 genomes]
rs9290098	0.92[ASN][1000 genomes]
rs9290099	0.92[ASN][1000 genomes]
rs9290100	0.92[ASN][1000 genomes]
rs9790050	0.92[ASN][1000 genomes]
rs9790137	0.92[ASN][1000 genomes]
rs9790219	0.92[ASN][1000 genomes]
rs9818800	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9825818	0.80[ASN][1000 genomes]
rs9829641	0.91[ASN][1000 genomes]
rs9829972	0.89[ASN][1000 genomes]
rs9834474	0.91[ASN][1000 genomes]
rs9834776	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9838918	0.90[ASN][1000 genomes]
rs9853434	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9856061	0.90[ASN][1000 genomes]
rs9860005	0.92[ASN][1000 genomes]
rs9874401	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751965	chr3:100299310-100462527	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	esv2751966	chr3:100299310-100468500	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv2756284	chr3:100299329-100427937	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2752830	chr3:100299329-100442478	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv432464	chr3:100299329-100442478	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv2751967	chr3:100299329-100455139	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv2751968	chr3:100299329-100476713	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv432466	chr3:100299329-100476713	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv536667	chr3:100308355-100445857	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv460770	chr3:100310812-100433592	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv591150	chr3:100310812-100433592	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv2751969	chr3:100312499-100479384	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	esv2763708	chr3:100317928-100442509	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv591151	chr3:100322043-100433592	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9856338	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL
rs9856338	IMPG2	cis	cerebellum	SCAN
rs9856338	TMEM45A	cis	parietal	SCAN
rs9856338	OR5K4	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100318200-100324200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:100318800-100323200	Enhancers	HMEC	breast
3	chr3:100319000-100323000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:100319400-100322200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:100319800-100322200	Weak transcription	Fetal Thymus	thymus
6	chr3:100319800-100322800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:100320000-100322600	Weak transcription	Esophagus	oesophagus
8	chr3:100320200-100322800	Enhancers	NHEK	skin
9	chr3:100320400-100322200	Enhancers	Liver	Liver
10	chr3:100320600-100323000	Enhancers	Fetal Intestine Small	intestine
11	chr3:100320800-100323000	Enhancers	Fetal Intestine Large	intestine
12	chr3:100321000-100322600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr3:100321000-100322800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:100321200-100322200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:100321200-100322400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr3:100321200-100322400	Flanking Active TSS	HepG2	liver
17	chr3:100321200-100322600	Enhancers	Muscle Satellite Cultured Cells	--
18	chr3:100321200-100322600	Enhancers	Hela-S3	cervix
19	chr3:100321200-100322600	Enhancers	NHDF-Ad	bronchial
20	chr3:100321200-100322800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:100321200-100322800	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr3:100321200-100322800	Enhancers	Stomach Mucosa	stomach
23	chr3:100321200-100322800	Enhancers	HSMMtube	muscle
24	chr3:100321200-100322800	Enhancers	K562	blood
25	chr3:100321200-100323000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr3:100321400-100322600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:100321400-100322800	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr3:100321400-100322800	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr3:100321400-100322800	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr3:100321400-100322800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:100321400-100322800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:100321400-100322800	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr3:100321400-100324200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:100321600-100322200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:100321600-100322400	Flanking Active TSS	A549	lung
36	chr3:100321600-100322600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:100321600-100322600	Flanking Active TSS	Primary B cells from peripheral blood	blood
38	chr3:100321600-100322600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:100321600-100322600	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr3:100321600-100322600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr3:100321600-100322800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:100321600-100323000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr3:100321800-100322200	Active TSS	Primary monocytes fromperipheralblood	blood
44	chr3:100321800-100322200	Active TSS	Primary B cells from cord blood	blood
45	chr3:100321800-100322200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:100321800-100322200	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr3:100321800-100322200	Active TSS	GM12878-XiMat	blood
48	chr3:100321800-100322200	Active TSS	NHLF	lung
49	chr3:100321800-100322400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr3:100321800-100322400	Active TSS	Brain Hippocampus Middle	brain

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