Variant report

Variant	rs7785392
Chromosome Location	chr7:99747378-99747379
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99745576-99747499	SK-N-MC	brain:	n/a	n/a
2	HCFC1	chr7:99745930-99747565	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr7:99745829-99747396	GM12878	blood:	n/a	n/a
4	JUN	chr7:99745805-99747561	K562	blood:	n/a	chr7:99746137-99746146
5	MXI1	chr7:99745662-99747561	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr7:99745804-99747481	GM12891	blood:	n/a	n/a
7	NR2F2	chr7:99745801-99747458	K562	blood:	n/a	n/a
8	MTA3	chr7:99745812-99747487	GM12878	blood:	n/a	n/a
9	POLR2A	chr7:99745973-99747381	H1-neurons	neurons:	n/a	n/a
10	MAZ	chr7:99745857-99747393	IMR90	lung:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
11	BHLHE40	chr7:99746080-99747421	K562	blood:	n/a	chr7:99746525-99746534 chr7:99746525-99746534
12	SIN3AK20	chr7:99745772-99747515	MCF-7	breast:	n/a	n/a
13	POLR2A	chr7:99745918-99747379	GM12892	blood:	n/a	n/a
14	POLR2A	chr7:99745923-99747490	SK-N-SH	brain:	n/a	n/a
15	NRF1	chr7:99745911-99747383	SK-N-SH	brain:	n/a	chr7:99746608-99746619
16	STAT5A	chr7:99746477-99747447	GM12878	blood:	n/a	n/a
17	STAT5A	chr7:99747051-99747417	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:99734202..99739266-chr7:99744673..99748688,7	MCF-7	breast:
2	chr7:99715646..99718646-chr7:99744846..99747972,4	MCF-7	breast:
3	chr7:99723048..99726558-chr7:99745237..99748437,5	K562	blood:
4	chr7:99678150..99680840-chr7:99745802..99747768,2	K562	blood:
5	chr7:99717232..99719759-chr7:99745742..99747993,2	MCF-7	breast:
6	chr7:99722705..99725740-chr7:99745468..99748073,3	K562	blood:
7	chr7:99745511..99748040-chr7:99809267..99811160,3	MCF-7	breast:
8	chr7:99743864..99749368-chr7:100025322..100029105,6	K562	blood:
9	chr7:99746174..99748056-chr7:99869608..99872452,2	K562	blood:
10	chr7:99697950..99701090-chr7:99746543..99749524,3	MCF-7	breast:
11	chr7:99723026..99726307-chr7:99744266..99747542,3	MCF-7	breast:
12	chr7:99679340..99681053-chr7:99745802..99747683,2	K562	blood:
13	chr7:99746381..99748629-chr7:100026351..100029105,2	K562	blood:
14	chr7:99735323..99737033-chr7:99747099..99749402,2	K562	blood:
15	chr7:99744806..99747397-chr7:99797049..99799857,2	K562	blood:

No data

Variant related genes	Relation type
LAMTOR4	TF binding region
ENSG00000146834	Chromatin interaction
ENSG00000214309	Chromatin interaction
ENSG00000106290	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000166526	Chromatin interaction
ENSG00000214142	Chromatin interaction
ENSG00000239521	Chromatin interaction
ENSG00000221838	Chromatin interaction
ENSG00000066923	Chromatin interaction
ENSG00000166508	Chromatin interaction
ENSG00000166997	Chromatin interaction
ENSG00000242798	Chromatin interaction
ENSG00000160844	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10231604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11771167	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12878	0.88[GIH][hapmap];0.92[MEX][hapmap];0.84[ASN][1000 genomes]
rs1527423	0.89[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap]
rs1918352	0.83[EUR][1000 genomes]
rs1918353	1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2272337	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2405440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35042434	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3736591	0.88[GIH][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs3779047	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7787294	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7787492	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7807641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs999885	0.85[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7785392	AP4M1	cis	lymphoblastoid	seeQTL
rs7785392	AP4M1	cis	multi-tissue	Pritchard
rs7785392	ZSCAN21	cis	parietal	SCAN
rs7785392	AP4M1	cis	Artery Tibial	GTEx
rs7785392	AP4M1	cis	cerebellum	SCAN
rs7785392	ZKSCAN1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99745800-99747400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr7:99745800-99747400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr7:99745800-99747400	Active TSS	Fetal Stomach	stomach
4	chr7:99745800-99747600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr7:99745800-99747600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:99745800-99747600	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr7:99745800-99747800	Active TSS	Fetal Kidney	kidney
8	chr7:99745800-99748200	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr7:99746000-99747400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr7:99746000-99747400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr7:99746000-99747400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:99746000-99747400	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr7:99746000-99747400	Active TSS	Esophagus	oesophagus
14	chr7:99746000-99747400	Active TSS	Gastric	stomach
15	chr7:99746000-99747400	Active TSS	Lung	lung
16	chr7:99746000-99747400	Active TSS	Ovary	ovary
17	chr7:99746000-99747400	Active TSS	Pancreas	Pancrea
18	chr7:99746000-99747400	Active TSS	Psoas Muscle	Psoas
19	chr7:99746000-99747400	Active TSS	Sigmoid Colon	Sigmoid Colon
20	chr7:99746000-99747600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr7:99746000-99747600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:99746000-99747600	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr7:99746000-99747600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:99746000-99747600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr7:99746000-99747600	Active TSS	NHDF-Ad	bronchial
26	chr7:99746000-99747800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr7:99746000-99748200	Active TSS	A549	lung
28	chr7:99746200-99747400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:99746200-99747400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr7:99746200-99747400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr7:99746200-99747400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr7:99746200-99747400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:99746200-99747400	Active TSS	Thymus	Thymus
34	chr7:99746200-99747400	Active TSS	HSMM	muscle
35	chr7:99746200-99747400	Active TSS	HSMMtube	muscle
36	chr7:99746200-99747600	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr7:99746200-99747600	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr7:99746200-99747600	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr7:99746200-99747600	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr7:99746200-99747600	Active TSS	Muscle Satellite Cultured Cells	--
41	chr7:99746200-99747600	Active TSS	Brain Anterior Caudate	brain
42	chr7:99746200-99747600	Active TSS	Fetal Intestine Large	intestine
43	chr7:99746200-99747600	Active TSS	Fetal Intestine Small	intestine
44	chr7:99746200-99747600	Active TSS	Hela-S3	cervix
45	chr7:99746200-99747600	Active TSS	NH-A	brain
46	chr7:99746200-99747800	Active TSS	H1 Cell Line	embryonic stem cell
47	chr7:99746200-99747800	Active TSS	GM12878-XiMat	blood
48	chr7:99746200-99748000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr7:99746200-99748000	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr7:99746400-99747600	Active TSS	HMEC	breast

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