Variant report

Variant	rs999886
Chromosome Location	chr7:99700864-99700865
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr7:99700740-99701395	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr7:99700701-99701994	SK-N-SH	brain:	n/a	n/a
3	RAD21	chr7:99700854-99701274	IMR90	lung:	n/a	n/a
4	RCOR1	chr7:99700354-99701372	IMR90	lung:	n/a	n/a
5	POLR2A	chr7:99700813-99700957	HepG2	liver:	n/a	n/a
6	MAZ	chr7:99700719-99701842	IMR90	lung:	n/a	n/a
7	FOSL2	chr7:99700649-99701417	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr7:99700622-99701170	IMR90	lung:	n/a	n/a
9	JUND	chr7:99700831-99701031	K562	blood:	n/a	chr7:99700947-99700958
10	POLR2A	chr7:99700694-99701324	HUVEC	blood vessel:	n/a	n/a
11	PBX3	chr7:99700773-99701553	SK-N-SH	brain:	n/a	n/a
12	JUND	chr7:99697410-99701902	SK-N-SH	brain:	n/a	chr7:99697600-99697609 chr7:99699066-99699075 chr7:99700947-99700958
13	MXI1	chr7:99697803-99701234	IMR90	lung:	n/a	chr7:99699039-99699048
14	POLR2A	chr7:99700770-99701322	SK-N-SH	brain:	n/a	n/a
15	PBX3	chr7:99700777-99701477	SK-N-SH	brain:	n/a	n/a
16	EP300	chr7:99700838-99701322	SK-N-SH_RA	brain:	n/a	n/a
17	FOSL1	chr7:99700682-99701170	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:99696160..99700887-chr7:99753963..99757907,5	K562	blood:
2	chr7:99516652..99519200-chr7:99698709..99701368,2	MCF-7	breast:
3	chr7:99699304..99700877-chr7:99754815..99757179,2	K562	blood:
4	chr7:99697950..99701090-chr7:99746543..99749524,3	MCF-7	breast:
5	chr7:99697437..99703178-chr7:100024624..100029482,10	K562	blood:

Variant related genes	Relation type
AP4M1	TF binding region
MCM7	TF binding region
ENSG00000146834	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000188186	Chromatin interaction
ENSG00000146833	Chromatin interaction
ENSG00000266154	Chromatin interaction
ENSG00000146826	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1050542	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1141057	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11550034	0.85[ASN][1000 genomes]
rs12112428	0.86[ASN][1000 genomes]
rs12112642	0.86[ASN][1000 genomes]
rs12534494	0.86[ASN][1000 genomes]
rs13309	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1534309	0.90[ASN][1000 genomes]
rs2272338	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2285886	0.86[ASN][1000 genomes]
rs2293481	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34161112	0.81[ASN][1000 genomes]
rs35058708	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35414630	0.81[ASN][1000 genomes]
rs3807479	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4134888	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4134917	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4134923	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4729567	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4729568	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4729571	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4729572	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4729577	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62485010	0.90[ASN][1000 genomes]
rs62485013	0.90[ASN][1000 genomes]
rs6960432	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs941290	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
7	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
8	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs999886	ZKSCAN1	cis	multi-tissue	Pritchard
rs999886	AP4M1	cis	Stomach	GTEx
rs999886	AP4M1	cis	Nerve Tibial	GTEx
rs999886	AP4M1	cis	Artery Tibial	GTEx
rs999886	AP4M1	cis	Adipose Subcutaneous	GTEx
rs999886	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs999886	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs999886	TAF6	cis	Thyroid	GTEx
rs999886	AP4M1	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99699800-99701000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr7:99699800-99703800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr7:99700000-99701400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr7:99700200-99701000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:99700200-99701000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr7:99700200-99701000	Enhancers	Gastric	stomach
7	chr7:99700200-99701000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr7:99700200-99701400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:99700200-99701800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr7:99700200-99702600	Weak transcription	Primary T cells from cord blood	blood
11	chr7:99700200-99702600	Weak transcription	Liver	Liver
12	chr7:99700200-99702800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr7:99700200-99702800	Weak transcription	Aorta	Aorta
14	chr7:99700200-99703200	Weak transcription	Primary B cells from cord blood	blood
15	chr7:99700200-99703600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:99700200-99709400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:99700200-99716200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr7:99700200-99716400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr7:99700400-99701000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr7:99700400-99701000	Weak transcription	Fetal Intestine Large	intestine
21	chr7:99700400-99701200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr7:99700400-99701200	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr7:99700400-99701200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
24	chr7:99700400-99701200	Genic enhancers	Stomach Smooth Muscle	stomach
25	chr7:99700400-99701400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
26	chr7:99700400-99701400	Weak transcription	Adipose Nuclei	Adipose
27	chr7:99700400-99701800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr7:99700400-99702400	Weak transcription	Brain Anterior Caudate	brain
29	chr7:99700400-99702600	Weak transcription	Brain Substantia Nigra	brain
30	chr7:99700400-99703400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr7:99700400-99703400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr7:99700400-99703800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr7:99700400-99703800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr7:99700400-99704400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr7:99700400-99704400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr7:99700400-99704400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr7:99700400-99705200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr7:99700400-99705800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr7:99700400-99705800	Weak transcription	GM12878-XiMat	blood
40	chr7:99700400-99707000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr7:99700400-99707400	Weak transcription	Fetal Kidney	kidney
42	chr7:99700400-99715800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr7:99700400-99716000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr7:99700400-99716200	Weak transcription	Psoas Muscle	Psoas
45	chr7:99700400-99716200	Weak transcription	Small Intestine	intestine
46	chr7:99700600-99701000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr7:99700600-99701000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr7:99700600-99701000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr7:99700600-99701000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr7:99700600-99701000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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