Variant report

Variant	rs9450304
Chromosome Location	chr6:86329859-86329860
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:86326265-86331930	K562	blood:	n/a	n/a
2	POLR2A	chr6:86329375-86330202	K562	blood:	n/a	n/a
3	POLR2A	chr6:86329258-86330020	GM12892	blood:	n/a	n/a
4	POLR2A	chr6:86329310-86329980	GM12891	blood:	n/a	n/a
5	POLR2A	chr6:86328853-86330582	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:86328534-86331146	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr6:86328891-86330008	K562	blood:	n/a	n/a
8	POLR2A	chr6:86328536-86331980	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:86328769-86329998	K562	blood:	n/a	n/a
10	POLR2A	chr6:86329238-86329946	GM12892	blood:	n/a	n/a
11	POLR2A	chr6:86329426-86330070	GM12892	blood:	n/a	n/a
12	POLR2A	chr6:86329377-86330478	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr6:86329277-86330013	GM12891	blood:	n/a	n/a
14	POLR2A	chr6:86329332-86329860	GM12891	blood:	n/a	n/a
15	POLR2A	chr6:86329309-86329908	MCF-7	breast:	n/a	n/a
16	POLR2A	chr6:86329261-86330820	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr6:86329420-86329962	HepG2	liver:	n/a	n/a
18	POLR2A	chr6:86329172-86330525	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:86329702-86329940	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr6:86329820-86329928	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:86329322-86329976	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr6:86329148-86330556	GM12892	blood:	n/a	n/a
23	POLR2A	chr6:86329265-86329874	SK-N-MC	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:86323280..86334231-chr6:86380512..86390230,24	K562	blood:
2	chr6:86322674..86325673-chr6:86325783..86329976,4	MCF-7	breast:
3	chr6:86319220..86322208-chr6:86328498..86330402,2	MCF-7	breast:
4	chr6:86324041..86326857-chr6:86327434..86330198,2	K562	blood:
5	chr6:86324041..86327385-chr6:86327434..86331742,5	K562	blood:
6	chr6:86314714..86316790-chr6:86327729..86330292,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000271793	TF binding region
ENSG00000271793	Chromatin interaction
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12528808	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2229524	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3812137	0.81[ASN][1000 genomes]
rs3812139	0.81[ASN][1000 genomes]
rs4327657	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59744370	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6900270	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6902638	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902904	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6910543	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6913634	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6923017	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930543	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6930790	0.87[ASN][1000 genomes]
rs73751215	0.81[ASN][1000 genomes]
rs7744309	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7749600	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752105	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7771187	0.81[ASN][1000 genomes]
rs7771366	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7775788	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344530	0.81[ASN][1000 genomes]
rs9344538	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9351063	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9351066	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9353319	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9353321	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9353323	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9353324	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9362223	0.81[ASN][1000 genomes]
rs9362225	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9362226	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444353	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9444356	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450286	0.81[ASN][1000 genomes]
rs9450289	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450294	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450295	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450299	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9450300	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450307	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450308	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450309	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450313	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
4	esv1792638	chr6:86224053-86336300	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv5383	chr6:86303223-86348023	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9450304	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs9450304	NT5E	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86304600-86331400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:86305800-86336200	Weak transcription	Fetal Heart	heart
3	chr6:86307600-86331000	Strong transcription	HSMM	muscle
4	chr6:86313400-86349000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:86313600-86338400	Strong transcription	GM12878-XiMat	blood
6	chr6:86313800-86340200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:86314200-86338200	Strong transcription	Dnd41	blood
8	chr6:86314200-86341200	Strong transcription	HMEC	breast
9	chr6:86314600-86334600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:86314800-86348600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:86315000-86330000	Strong transcription	Osteobl	bone
12	chr6:86315000-86347800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:86315200-86338200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:86315400-86338200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:86315400-86338200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:86315400-86347400	Strong transcription	HUVEC	blood vessel
17	chr6:86315600-86330200	Strong transcription	NH-A	brain
18	chr6:86315600-86331000	Strong transcription	NHDF-Ad	bronchial
19	chr6:86315800-86330400	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr6:86316000-86348600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr6:86316200-86339200	Strong transcription	Primary B cells from cord blood	blood
22	chr6:86316200-86347800	Strong transcription	Duodenum Mucosa	Duodenum
23	chr6:86316200-86348600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr6:86316200-86348600	Strong transcription	Placenta	Placenta
25	chr6:86316200-86348800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:86316400-86348200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:86316400-86348400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:86316400-86349200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr6:86316400-86350600	Strong transcription	Fetal Thymus	thymus
30	chr6:86317000-86337400	Strong transcription	Primary T cells from cord blood	blood
31	chr6:86317000-86340400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:86317000-86349000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:86317400-86338800	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr6:86317400-86349000	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:86317600-86349800	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr6:86317800-86337600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr6:86317800-86348200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr6:86318600-86348800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr6:86318800-86347200	Strong transcription	Fetal Brain Female	brain
40	chr6:86319000-86333800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr6:86319000-86350000	Strong transcription	Fetal Muscle Trunk	muscle
42	chr6:86319200-86330200	Strong transcription	NHLF	lung
43	chr6:86319200-86333600	Strong transcription	Adipose Nuclei	Adipose
44	chr6:86319400-86348600	Strong transcription	K562	blood
45	chr6:86319600-86342400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr6:86319600-86348200	Strong transcription	NHEK	skin
47	chr6:86319600-86348800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:86319600-86350000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr6:86320000-86344200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:86320000-86348600	Strong transcription	Liver	Liver

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