Variant report

Variant	rs2859420
Chromosome Location	chr6:35803283-35803284
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	chr6:35802976..35805287-chr6:35807209..35809542,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10484264	0.81[GIH][hapmap]
rs1049649	0.85[CEU][hapmap];0.83[GIH][hapmap];0.81[EUR][1000 genomes]
rs10947572	0.82[CEU][hapmap]
rs1160828	0.85[CEU][hapmap]
rs11755072	0.85[CEU][hapmap]
rs1326752	0.85[CEU][hapmap]
rs17653835	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs17705020	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs2038961	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2038962	0.80[EUR][1000 genomes]
rs2051647	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs2301510	0.85[CEU][hapmap]
rs2395638	0.80[EUR][1000 genomes]
rs2395640	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs2766522	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2766527	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2766528	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2817019	0.82[EUR][1000 genomes]
rs2817027	0.82[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap]
rs3213580	0.86[CEU][hapmap]
rs3761981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3891863	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs4340986	0.85[CEU][hapmap];0.83[GIH][hapmap];0.80[EUR][1000 genomes]
rs4713929	0.89[EUR][1000 genomes]
rs608267	0.80[EUR][1000 genomes]
rs612262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs638600	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs639421	0.85[CEU][hapmap];0.81[GIH][hapmap]
rs6457858	0.82[CEU][hapmap];0.83[GIH][hapmap];0.80[EUR][1000 genomes]
rs6457859	0.81[EUR][1000 genomes]
rs6457860	0.81[EUR][1000 genomes]
rs6457862	0.85[CEU][hapmap];0.83[GIH][hapmap];0.80[EUR][1000 genomes]
rs651158	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs662713	0.82[CEU][hapmap]
rs677937	0.85[CEU][hapmap]
rs6908433	0.85[CEU][hapmap]
rs6909895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6910906	0.80[EUR][1000 genomes]
rs6911849	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs6916941	0.91[CEU][hapmap]
rs6920616	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6920862	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6922695	0.80[EUR][1000 genomes]
rs6923015	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.81[EUR][1000 genomes]
rs6929493	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs6931888	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs6932973	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs6933241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs721694	0.80[EUR][1000 genomes]
rs7740886	0.82[CEU][hapmap];0.83[GIH][hapmap]
rs7744924	0.80[EUR][1000 genomes]
rs7752545	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs7752551	0.85[CEU][hapmap];0.83[GIH][hapmap];0.80[EUR][1000 genomes]
rs7755022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7755600	0.85[CEU][hapmap]
rs7758042	0.83[GIH][hapmap]
rs7774060	0.80[EUR][1000 genomes]
rs879493	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs879667	0.81[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9296168	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap]
rs9462125	0.80[EUR][1000 genomes]
rs9462127	0.80[EUR][1000 genomes]
rs9462128	0.85[CEU][hapmap];0.82[GIH][hapmap];0.81[EUR][1000 genomes]
rs9462131	0.80[EUR][1000 genomes]
rs9462132	0.85[CEU][hapmap];0.83[GIH][hapmap];0.80[EUR][1000 genomes]
rs9462133	0.80[EUR][1000 genomes]
rs9462134	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs9462135	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs9462136	0.83[GIH][hapmap]
rs9462141	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9462143	0.85[CEU][hapmap]
rs9470111	0.80[EUR][1000 genomes]
rs9470119	0.80[EUR][1000 genomes]
rs9470120	0.85[CEU][hapmap];0.83[GIH][hapmap];0.81[EUR][1000 genomes]
rs9470121	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9470122	0.81[EUR][1000 genomes]
rs9470123	0.81[EUR][1000 genomes]
rs9470125	0.81[EUR][1000 genomes]
rs9470126	0.85[CEU][hapmap];0.83[GIH][hapmap];0.80[EUR][1000 genomes]
rs9470131	0.85[CEU][hapmap];0.83[GIH][hapmap];0.80[EUR][1000 genomes]
rs9470134	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470136	0.80[EUR][1000 genomes]
rs9470138	0.85[CEU][hapmap];0.83[GIH][hapmap];0.80[EUR][1000 genomes]
rs9470139	0.85[CEU][hapmap];0.83[GIH][hapmap];0.80[EUR][1000 genomes]
rs9470141	0.85[CEU][hapmap]
rs9470144	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9470147	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap]
rs9470152	0.85[CEU][hapmap]
rs9470153	0.85[CEU][hapmap]
rs9470154	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9470155	0.85[CEU][hapmap];0.81[GIH][hapmap]
rs9470156	0.84[CEU][hapmap]
rs9470162	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs9470171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9470172	0.85[CEU][hapmap];0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv885803	chr6:35621781-35805133	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv885804	chr6:35621781-35809776	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv428143	chr6:35637083-35806504	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	esv1791730	chr6:35754783-35805144	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2859420	BRPF3	cis	cerebellum	SCAN
rs2859420	SRPK1	cis	parietal	SCAN
rs2859420	C6orf106	cis	cerebellum	SCAN
rs2859420	SRPK1	cis	cerebellum	SCAN
rs2859420	CDKN1A	cis	cerebellum	SCAN
rs2859420	LHFPL5	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35787800-35855600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:35791400-35824200	Weak transcription	Fetal Brain Male	brain
3	chr6:35791600-35819800	Weak transcription	NHLF	lung
4	chr6:35793400-35805000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:35798200-35823800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr6:35799200-35806600	Weak transcription	Fetal Heart	heart
7	chr6:35799400-35808600	Weak transcription	Fetal Lung	lung
8	chr6:35799600-35837200	Weak transcription	Fetal Kidney	kidney
9	chr6:35799800-35804200	Weak transcription	Fetal Muscle Leg	muscle
10	chr6:35799800-35805200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:35799800-35823000	Weak transcription	Colonic Mucosa	Colon
12	chr6:35800000-35805000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:35800000-35806000	Weak transcription	Brain Anterior Caudate	brain
14	chr6:35800000-35816200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:35800000-35823800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:35800400-35806800	Strong transcription	GM12878-XiMat	blood
17	chr6:35800400-35810800	Strong transcription	Hela-S3	cervix
18	chr6:35800400-35810800	Strong transcription	NH-A	brain
19	chr6:35800400-35816000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:35800400-35816200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:35800400-35816400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:35800600-35803600	Strong transcription	Fetal Brain Female	brain
23	chr6:35800600-35803800	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr6:35800600-35804400	Genic enhancers	Primary B cells from cord blood	blood
25	chr6:35800600-35805600	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr6:35800600-35807000	Strong transcription	HUVEC	blood vessel
27	chr6:35800600-35807200	Strong transcription	Brain Germinal Matrix	brain
28	chr6:35800600-35809400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:35800600-35810600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:35800600-35810800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:35800600-35816400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:35800600-35816400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:35800600-35859000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:35800800-35807000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:35800800-35809000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:35801000-35803600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:35801000-35804000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:35801000-35804000	Strong transcription	Fetal Intestine Large	intestine
39	chr6:35801000-35809400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr6:35801000-35810400	Strong transcription	Duodenum Mucosa	Duodenum
41	chr6:35801000-35810600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr6:35801000-35813800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:35801000-35832600	Strong transcription	Fetal Thymus	thymus
44	chr6:35801000-35840600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:35801200-35803400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr6:35801200-35803400	Strong transcription	Adipose Nuclei	Adipose
47	chr6:35801200-35804200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr6:35801200-35804400	Strong transcription	A549	lung
49	chr6:35801200-35805000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:35801200-35807000	Strong transcription	HMEC	breast

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