Variant report

Variant	rs999885
Chromosome Location	chr7:99701176-99701177
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	POLR2A	chr7:99701070-99701223	HUVEC	blood vessel:	n/a	n/a
5	RCOR1	chr7:99700354-99701372	IMR90	lung:	n/a	n/a
6	MAFK	chr7:99700922-99701230	IMR90	lung:	n/a	n/a
7	MAZ	chr7:99700719-99701842	IMR90	lung:	n/a	n/a
8	FOSL2	chr7:99700649-99701417	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr7:99700694-99701324	HUVEC	blood vessel:	n/a	n/a
10	PBX3	chr7:99700773-99701553	SK-N-SH	brain:	n/a	n/a
11	JUND	chr7:99697410-99701902	SK-N-SH	brain:	n/a	chr7:99697600-99697609 chr7:99699066-99699075 chr7:99700947-99700958
12	MXI1	chr7:99697803-99701234	IMR90	lung:	n/a	chr7:99699039-99699048
13	PBX3	chr7:99701088-99701281	GM12878	blood:	n/a	n/a
14	CEBPB	chr7:99700921-99701327	IMR90	lung:	n/a	n/a
15	POLR2A	chr7:99700770-99701322	SK-N-SH	brain:	n/a	n/a
16	PBX3	chr7:99700777-99701477	SK-N-SH	brain:	n/a	n/a
17	EP300	chr7:99700838-99701322	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99516652..99519200-chr7:99698709..99701368,2	MCF-7	breast:
2	chr7:99697437..99703178-chr7:100024624..100029482,10	K562	blood:

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

Extended variants
information (count: 34 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10231604	0.85[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap]
rs10281368	0.91[YRI][hapmap]
rs11764584	0.85[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap]
rs11771139	0.95[YRI][hapmap]
rs13223792	0.81[YRI][hapmap]
rs1527423	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1880949	0.95[YRI][hapmap]
rs1918353	0.85[CEU][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap]
rs2272337	0.81[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap]
rs2272338	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs2293479	0.86[YRI][hapmap]
rs2405440	0.85[CEU][hapmap]
rs35146811	0.95[YRI][hapmap]
rs3736590	0.85[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap]
rs3800951	0.85[CEU][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap]
rs3823646	0.85[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap]
rs4134903	0.95[YRI][hapmap]
rs4134917	0.88[GIH][hapmap];0.87[MEX][hapmap]
rs4729567	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs4729568	0.87[MEX][hapmap]
rs4729577	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs6960432	0.81[GIH][hapmap];0.87[MEX][hapmap]
rs7785392	0.85[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap]
rs7807156	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807641	0.85[CEU][hapmap]
rs9649220	0.81[GIH][hapmap];0.87[MEX][hapmap]

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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs999885	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs999885	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs999885	GATS	cis	parietal	SCAN
rs999885	AP4M1	cis	cerebellum	SCAN
rs999885	AP4M1	cis	lymphoblastoid	seeQTL
rs999885	ZSCAN21	cis	parietal	SCAN
rs999885	TAF6	cis	Thyroid	GTEx
rs999885	AP4M1	cis	Artery Tibial	GTEx
rs999885	AP4M1	cis	Thyroid	GTEx
rs999885	ZKSCAN1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99699800-99703800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr7:99700000-99701400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:99700200-99701400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:99700200-99701800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr7:99700200-99702600	Weak transcription	Primary T cells from cord blood	blood
6	chr7:99700200-99702600	Weak transcription	Liver	Liver
7	chr7:99700200-99702800	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr7:99700200-99702800	Weak transcription	Aorta	Aorta
9	chr7:99700200-99703200	Weak transcription	Primary B cells from cord blood	blood
10	chr7:99700200-99703600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:99700200-99709400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr7:99700200-99716200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr7:99700200-99716400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:99700400-99701200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:99700400-99701200	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr7:99700400-99701200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
17	chr7:99700400-99701200	Genic enhancers	Stomach Smooth Muscle	stomach
18	chr7:99700400-99701400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
19	chr7:99700400-99701400	Weak transcription	Adipose Nuclei	Adipose
20	chr7:99700400-99701800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr7:99700400-99702400	Weak transcription	Brain Anterior Caudate	brain
22	chr7:99700400-99702600	Weak transcription	Brain Substantia Nigra	brain
23	chr7:99700400-99703400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr7:99700400-99703400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr7:99700400-99703800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr7:99700400-99703800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:99700400-99704400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr7:99700400-99704400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr7:99700400-99704400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr7:99700400-99705200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr7:99700400-99705800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr7:99700400-99705800	Weak transcription	GM12878-XiMat	blood
33	chr7:99700400-99707000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr7:99700400-99707400	Weak transcription	Fetal Kidney	kidney
35	chr7:99700400-99715800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr7:99700400-99716000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr7:99700400-99716200	Weak transcription	Psoas Muscle	Psoas
38	chr7:99700400-99716200	Weak transcription	Small Intestine	intestine
39	chr7:99700600-99701200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr7:99700600-99701200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr7:99700600-99701200	Genic enhancers	Brain Germinal Matrix	brain
42	chr7:99700600-99701200	Genic enhancers	Fetal Brain Female	brain
43	chr7:99700600-99701200	Genic enhancers	Dnd41	blood
44	chr7:99700600-99701200	Enhancers	K562	blood
45	chr7:99700600-99701200	Enhancers	NHDF-Ad	bronchial
46	chr7:99700600-99701200	Enhancers	NHLF	lung
47	chr7:99700600-99701400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:99700600-99701400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:99700600-99701400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr7:99700600-99701400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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