Variant report

Variant	rs6823013
Chromosome Location	chr4:76581064-76581065
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:76580627..76584350-chr4:76648394..76652351,4	K562	blood:
2	chr4:76580944..76583542-chr4:76596776..76599526,2	MCF-7	breast:
3	chr4:76578842..76581813-chr4:76628812..76631352,2	K562	blood:
4	chr4:76575310..76582874-chr4:76594032..76598652,8	K562	blood:
5	chr4:76579381..76581543-chr4:76596337..76599552,3	MCF-7	breast:
6	chr4:76572563..76577476-chr4:76578400..76583140,7	K562	blood:
7	chr4:76573131..76578046-chr4:76580054..76584668,6	K562	blood:
8	chr4:76578830..76581490-chr4:76590294..76592891,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000138768	Chromatin interaction
ENSG00000138757	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs17000766	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1801838	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017607	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2037012	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs324694	1.00[CHD][hapmap]
rs324706	1.00[CHD][hapmap]
rs324734	1.00[CHD][hapmap]
rs41398350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56084244	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56151783	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56308338	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56693719	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56728961	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57008925	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57099382	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58140957	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58822138	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59405026	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59448225	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59684133	0.84[AFR][1000 genomes]
rs60332325	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66606482	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67662392	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6812339	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs68155345	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6818849	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6821144	1.00[AMR][1000 genomes]
rs6828587	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841290	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6843244	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6857983	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72649405	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72649420	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv879495	chr4:76493256-76585823	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv879496	chr4:76493256-76620803	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv879497	chr4:76519096-76620803	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv1793652	chr4:76521217-76581775	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6823013	EXTL1	trans	cerebellum	SCAN
rs6823013	CSTB	trans	lymphoblastoid	seeQTL
rs6823013	FAM47E	cis	parietal	SCAN
rs6823013	SDAD1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76556200-76590000	Weak transcription	Small Intestine	intestine
2	chr4:76565000-76584200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:76565600-76588600	Strong transcription	Fetal Thymus	thymus
4	chr4:76565600-76588800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:76566200-76596600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:76566400-76593800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:76566800-76585800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:76567000-76588200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr4:76567000-76588200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr4:76567200-76585800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:76567200-76586200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:76567400-76587400	Strong transcription	Placenta	Placenta
13	chr4:76567400-76588400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:76567400-76588400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr4:76567400-76596600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:76567600-76587000	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr4:76567600-76587200	Strong transcription	Liver	Liver
18	chr4:76567600-76588000	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr4:76567600-76588200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr4:76567600-76588400	Strong transcription	Dnd41	blood
21	chr4:76568000-76583600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr4:76568000-76587400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:76568000-76588600	Strong transcription	Primary B cells from cord blood	blood
24	chr4:76568200-76584800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:76568600-76583600	Strong transcription	Adipose Nuclei	Adipose
26	chr4:76568600-76588600	Strong transcription	Primary B cells from peripheral blood	blood
27	chr4:76568800-76581200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr4:76568800-76583400	Strong transcription	Fetal Intestine Large	intestine
29	chr4:76568800-76584000	Strong transcription	NH-A	brain
30	chr4:76568800-76587800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr4:76569400-76584000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr4:76569600-76584000	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr4:76569600-76585000	Weak transcription	Stomach Mucosa	stomach
34	chr4:76569600-76586800	Strong transcription	Primary hematopoietic stem cells	blood
35	chr4:76569800-76588600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr4:76570000-76587200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr4:76570000-76588200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:76570600-76587200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:76571400-76586200	Weak transcription	Gastric	stomach
40	chr4:76571800-76590000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:76572000-76590000	Weak transcription	Pancreas	Pancrea
42	chr4:76572000-76592200	Weak transcription	Psoas Muscle	Psoas
43	chr4:76572000-76594400	Weak transcription	Aorta	Aorta
44	chr4:76572400-76582800	Weak transcription	Fetal Heart	heart
45	chr4:76572400-76585200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:76573200-76582600	Weak transcription	Fetal Brain Male	brain
47	chr4:76573800-76596200	Weak transcription	Colonic Mucosa	Colon
48	chr4:76574000-76582600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr4:76574000-76596400	Weak transcription	Right Ventricle	heart
50	chr4:76575600-76581200	Weak transcription	Fetal Muscle Leg	muscle

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