Variant report

Variant	rs4729571
Chromosome Location	chr7:99648267-99648268
allele	A/G
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99618852..99620390-chr7:99647489..99649484,2	MCF-7	breast:
2	chr7:99613224..99616757-chr7:99646903..99650456,6	K562	blood:
3	chr7:99612024..99615373-chr7:99646672..99650813,5	MCF-7	breast:
4	chr7:99645911..99648901-chr7:99677073..99680526,5	MCF-7	breast:
5	chr7:99587259..99592938-chr7:99645564..99652306,10	MCF-7	breast:
6	chr7:99614422..99616781-chr7:99647909..99649489,3	K562	blood:
7	chr7:99647023..99648949-chr7:99679217..99680887,2	K562	blood:
8	chr7:99643901..99648827-chr7:99678011..99681180,5	MCF-7	breast:
9	chr7:99645798..99648883-chr7:99696634..99699359,3	MCF-7	breast:
10	chr7:99646221..99648949-chr7:99678840..99680973,5	K562	blood:
11	chr7:99645952..99651427-chr7:99695296..99699701,5	K562	blood:
12	chr7:99647658..99649972-chr7:99695317..99698308,2	K562	blood:
13	chr7:99154927..99157797-chr7:99646384..99648528,2	K562	blood:
14	chr7:99516710..99519672-chr7:99647513..99649327,2	MCF-7	breast:
15	chr7:99643907..99646572-chr7:99647724..99651166,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272647	Chromatin interaction
ENSG00000166526	Chromatin interaction
ENSG00000221838	Chromatin interaction
ENSG00000197343	Chromatin interaction
ENSG00000146833	Chromatin interaction
ENSG00000166508	Chromatin interaction
ENSG00000235713	Chromatin interaction
ENSG00000106261	Chromatin interaction
ENSG00000221909	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1050542	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1141057	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12112428	0.90[ASN][1000 genomes]
rs12112642	0.90[ASN][1000 genomes]
rs12534494	0.90[ASN][1000 genomes]
rs13309	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1534309	0.83[ASN][1000 genomes]
rs2272338	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2285886	0.90[ASN][1000 genomes]
rs2293481	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35058708	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35414630	0.85[ASN][1000 genomes]
rs3807479	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4134888	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4134917	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4134923	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4729567	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4729568	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4729572	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4729577	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62485010	0.83[ASN][1000 genomes]
rs6960432	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs941290	0.83[ASN][1000 genomes]
rs999886	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[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	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4729571	TAF6	cis	Thyroid	GTEx
rs4729571	AP4M1	cis	Esophagus Muscularis	GTEx
rs4729571	AP4M1	cis	Nerve Tibial	GTEx
rs4729571	AP4M1	cis	Artery Tibial	GTEx
rs4729571	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs4729571	AP4M1	cis	Whole Blood	GTEx
rs4729571	AP4M1	cis	Adipose Subcutaneous	GTEx
rs4729571	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs4729571	AP4M1	cis	Stomach	GTEx
rs4729571	ZKSCAN1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99646600-99648400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr7:99646600-99648400	Active TSS	Rectal Smooth Muscle	rectum
3	chr7:99646800-99648400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr7:99646800-99648400	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr7:99646800-99648400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr7:99646800-99648600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr7:99646800-99648600	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr7:99647000-99648400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr7:99647000-99648400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr7:99647000-99648400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr7:99647000-99648600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr7:99647000-99648600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:99647000-99648600	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr7:99647200-99648400	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr7:99647200-99648400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:99647200-99648400	Active TSS	Brain Germinal Matrix	brain
17	chr7:99647200-99648400	Active TSS	HSMMtube	muscle
18	chr7:99647200-99648400	Active TSS	NHDF-Ad	bronchial
19	chr7:99647200-99648600	Active TSS	HSMM	muscle
20	chr7:99647600-99648400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr7:99647600-99648400	Flanking Active TSS	Liver	Liver
22	chr7:99647800-99648400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr7:99647800-99648400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:99647800-99648400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr7:99647800-99648400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr7:99647800-99648400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:99647800-99648400	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr7:99647800-99648400	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr7:99647800-99648400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr7:99647800-99648400	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr7:99647800-99648400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr7:99647800-99648400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr7:99647800-99648400	Flanking Active TSS	Fetal Muscle Leg	muscle
34	chr7:99647800-99648400	Flanking Active TSS	Fetal Stomach	stomach
35	chr7:99647800-99648400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr7:99647800-99648600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr7:99647800-99648600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:99647800-99648600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr7:99647800-99648600	Enhancers	Spleen	Spleen
40	chr7:99647800-99648600	Flanking Active TSS	Dnd41	blood
41	chr7:99648000-99648400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
42	chr7:99648000-99648400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr7:99648000-99648400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr7:99648000-99648400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr7:99648000-99648400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:99648000-99648400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr7:99648000-99648400	Enhancers	Primary B cells from cord blood	blood
48	chr7:99648000-99648400	Enhancers	Primary B cells from peripheral blood	blood
49	chr7:99648000-99648400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr7:99648000-99648400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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