Variant report

Variant	rs9856298
Chromosome Location	chr3:133957265-133957266
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:133956480..133959518-chr3:133968010..133971200,3	MCF-7	breast:
2	chr3:133955309..133957526-chr3:133961542..133964023,3	K562	blood:
3	chr3:133951157..133954155-chr3:133956985..133958917,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163785	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10804630	0.88[GIH][hapmap];0.93[MEX][hapmap]
rs10935104	0.93[CEU][hapmap]
rs1131262	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11707763	0.87[ASN][1000 genomes]
rs11915143	0.87[ASN][1000 genomes]
rs35322473	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3890774	0.90[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4072180	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4324466	0.88[ASN][1000 genomes]
rs4682664	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682666	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682668	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4682669	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55689708	0.80[ASN][1000 genomes]
rs56073423	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439465	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6439466	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6650893	0.88[ASN][1000 genomes]
rs6762690	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6776502	0.92[CEU][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6780295	0.88[ASN][1000 genomes]
rs6800143	0.88[ASN][1000 genomes]
rs6808085	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7355922	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7609611	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7622046	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9283588	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9812461	0.85[ASN][1000 genomes]
rs9818714	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823873	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9825808	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9827728	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9832732	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9839819	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9853568	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9856792	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858069	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858450	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9858707	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	esv1794616	chr3:133949713-133973731	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription 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	14 gene(s)	inside rSNPs	diseases
4	esv1798974	chr3:133949713-133973731	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
5	esv1802675	chr3:133949713-133973731	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv1815799	chr3:133949713-133973731	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	esv1819695	chr3:133949713-133973731	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	esv1822126	chr3:133949713-133973731	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
9	esv1839030	chr3:133949713-133973731	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9856298	PIK3CB	cis	parietal	SCAN
rs9856298	DBR1	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133930200-133968000	Weak transcription	Fetal Kidney	kidney
2	chr3:133930600-133957800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:133941000-133961600	Weak transcription	Esophagus	oesophagus
4	chr3:133941400-133967400	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:133943400-133961800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:133943600-133957800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:133943600-133957800	Weak transcription	Lung	lung
8	chr3:133947200-133957800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:133949800-133959600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:133950600-133957800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr3:133950600-133961800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:133950800-133957800	Weak transcription	Left Ventricle	heart
13	chr3:133951200-133960600	Weak transcription	Thymus	Thymus
14	chr3:133951200-133966800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:133952000-133960400	Weak transcription	Hela-S3	cervix
16	chr3:133952200-133965400	Weak transcription	Dnd41	blood
17	chr3:133953000-133957400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr3:133953200-133957800	Enhancers	Colon Smooth Muscle	Colon
19	chr3:133953200-133959800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:133953200-133967800	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr3:133953400-133966800	Weak transcription	Brain Angular Gyrus	brain
22	chr3:133954400-133957400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr3:133954400-133957400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr3:133954400-133958800	Enhancers	HepG2	liver
25	chr3:133954400-133959600	Enhancers	NHDF-Ad	bronchial
26	chr3:133954600-133957400	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr3:133954600-133957600	Enhancers	Duodenum Mucosa	Duodenum
28	chr3:133954600-133957800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr3:133954600-133958600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:133954600-133958800	Enhancers	Liver	Liver
31	chr3:133954600-133958800	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr3:133954600-133958800	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr3:133954600-133959000	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr3:133954600-133959200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:133954600-133960000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr3:133954600-133960600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr3:133954600-133961600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr3:133954800-133958200	Weak transcription	Brain Substantia Nigra	brain
39	chr3:133954800-133958600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr3:133954800-133959800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:133954800-133962400	Weak transcription	Colonic Mucosa	Colon
42	chr3:133955000-133961800	Weak transcription	Aorta	Aorta
43	chr3:133955000-133962000	Weak transcription	Fetal Intestine Large	intestine
44	chr3:133955200-133958800	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr3:133955200-133960400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:133955200-133961600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr3:133955400-133957600	Enhancers	Stomach Smooth Muscle	stomach
48	chr3:133955400-133958200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:133955400-133958200	Enhancers	Stomach Mucosa	stomach
50	chr3:133955600-133957400	Enhancers	Fetal Lung	lung

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