Variant report

Variant	rs941290
Chromosome Location	chr7:99678622-99678623
allele	A/C
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	POLR2A	chr7:99678608-99679730	HepG2	liver:	n/a	n/a
2	POLR2A	chr7:99678449-99679676	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD2	chr7:99678587-99678826	K562	blood:	n/a	n/a
4	ZNF143	chr7:99678611-99678867	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:99678454-99679773	H1-neurons	neurons:	n/a	n/a
6	GABPA	chr7:99678431-99679861	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr7:99678430-99680094	A549	lung:	n/a	chr7:99679557-99679575 chr7:99679559-99679572 chr7:99679552-99679573 chr7:99679558-99679574 chr7:99679559-99679572
8	SIN3AK20	chr7:99678580-99679775	K562	blood:	n/a	n/a
9	POLR2A	chr7:99678590-99679838	HUVEC	blood vessel:	n/a	n/a
10	MAX	chr7:99678478-99679924	SK-N-SH	brain:	n/a	chr7:99679616-99679626
11	POLR2A	chr7:99678508-99680450	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr7:99677700-99679758	SK-N-SH	brain:	n/a	n/a
13	CREB1	chr7:99678479-99679818	HepG2	liver:	n/a	n/a
14	MAX	chr7:99678454-99679941	SK-N-SH	brain:	n/a	chr7:99679616-99679626
15	POLR2A	chr7:99678602-99678867	H1-hESC	embryonic stem cell:	n/a	n/a
16	TCF12	chr7:99678502-99678789	H1-hESC	embryonic stem cell:	n/a	chr7:99678760-99678768 chr7:99678719-99678726
17	POLR2A	chr7:99678616-99678786	GM12878	blood:	n/a	n/a
18	POLR2A	chr7:99678451-99679653	SK-N-SH	brain:	n/a	n/a
19	FOXA1	chr7:99678395-99679045	HepG2	liver:	n/a	chr7:99678632-99678647
20	NFIC	chr7:99678426-99678804	HepG2	liver:	n/a	n/a
21	POLR2A	chr7:99678548-99680550	K562	blood:	n/a	n/a
22	ELF1	chr7:99678453-99678802	HepG2	liver:	n/a	chr7:99678662-99678673 chr7:99678661-99678674
23	SREBP2	chr7:99678395-99681082	GM12878	blood:	n/a	n/a
24	POLR2A	chr7:99678439-99679765	IMR90	lung:	n/a	n/a
25	POLR2A	chr7:99678481-99679794	GM12878	blood:	n/a	n/a
26	POLR2A	chr7:99678581-99678893	HepG2	liver:	n/a	n/a
27	ARID3A	chr7:99678436-99679671	HepG2	liver:	n/a	n/a
28	GABPA	chr7:99678415-99679822	A549	lung:	n/a	n/a
29	GABPA	chr7:99678491-99679783	A549	lung:	n/a	n/a
30	SIN3A	chr7:99678496-99680583	H1-hESC	embryonic stem cell:	n/a	n/a
31	MYBL2	chr7:99678413-99678843	HepG2	liver:	n/a	n/a
32	FOXA1	chr7:99678518-99678726	T-47D	breast:	n/a	chr7:99678632-99678647
33	GABPA	chr7:99678402-99679958	MCF-7	breast:	n/a	n/a
34	POLR2A	chr7:99678480-99679745	GM12892	blood:	n/a	n/a
35	POLR2A	chr7:99678565-99678976	PANC-1	pancreas:	n/a	n/a
36	ELF1	chr7:99678445-99678861	HepG2	liver:	n/a	chr7:99678662-99678673 chr7:99678661-99678674
37	CBX3	chr7:99678541-99680048	K562	blood:	n/a	n/a
38	MXI1	chr7:99678495-99679782	HepG2	liver:	n/a	n/a
39	SIN3AK20	chr7:99678412-99679811	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr7:99678428-99679616	GM12878	blood:	n/a	n/a
41	POLR2A	chr7:99678581-99679733	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr7:99678617-99679645	MCF-7	breast:	n/a	n/a
43	TCF12	chr7:99678428-99679852	A549	lung:	n/a	chr7:99679475-99679485 chr7:99678760-99678768 chr7:99678719-99678726
44	POLR2A	chr7:99678473-99679511	HepG2	liver:	n/a	n/a
45	MAX	chr7:99678579-99678846	HepG2	liver:	n/a	n/a
46	MAX	chr7:99678527-99680024	HCT-116	colon:	n/a	chr7:99679616-99679626
47	CTCF	chr7:99678560-99678710	HUVEC	blood vessel:	n/a	n/a
48	SMC3	chr7:99678235-99680005	SK-N-SH	brain:	n/a	chr7:99679559-99679573
49	TAF1	chr7:99678498-99679795	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr7:99678501-99680454	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:99611430..99615857-chr7:99675156..99681193,15	K562	blood:
2	chr7:99677846..99681399-chr7:100025174..100029012,4	K562	blood:
3	chr7:99576524..99578899-chr7:99677600..99679193,2	K562	blood:
4	chr7:99677781..99680960-chr7:99753334..99755747,3	K562	blood:
5	chr7:99643901..99648827-chr7:99678011..99681180,5	MCF-7	breast:
6	chr7:99515767..99517509-chr7:99677745..99680762,3	K562	blood:
7	chr7:99034954..99037975-chr7:99677842..99679932,3	K562	blood:
8	chr7:99612275..99615910-chr7:99677885..99681193,8	K562	blood:
9	chr7:99668310..99676246-chr7:99677185..99681836,16	MCF-7	breast:
10	chr7:99095910..99098991-chr7:99677831..99680952,3	K562	blood:
11	chr7:99677604..99679757-chr7:100032184..100034035,2	K562	blood:
12	chr7:99515562..99518077-chr7:99677870..99680297,2	MCF-7	breast:
13	chr7:99645911..99648901-chr7:99677073..99680526,5	MCF-7	breast:
14	chr7:99612316..99614498-chr7:99678113..99681049,2	MCF-7	breast:
15	chr7:99034954..99037866-chr7:99677567..99679393,3	K562	blood:
16	chr7:99678150..99680840-chr7:99745802..99747768,2	K562	blood:
17	chr7:99677060..99680949-chr7:100024846..100027547,5	MCF-7	breast:

Variant related genes	Relation type
ZNF3	TF binding region
ENSG00000188186	Chromatin interaction
ENSG00000146833	Chromatin interaction
ENSG00000166526	Chromatin interaction
ENSG00000106261	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000160917	Chromatin interaction
ENSG00000266154	Chromatin interaction
ENSG00000240211	Chromatin interaction
ENSG00000214313	Chromatin interaction
ENSG00000146826	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000166529	Chromatin interaction
ENSG00000241357	Chromatin interaction
ENSG00000160813	Chromatin interaction
ENSG00000160908	Chromatin interaction
ENSG00000106246	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1050542	0.84[ASN][1000 genomes]
rs1141057	0.87[ASN][1000 genomes]
rs11550034	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12112428	0.84[ASN][1000 genomes]
rs12112642	0.84[ASN][1000 genomes]
rs12534494	0.84[ASN][1000 genomes]
rs13309	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1534309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1569055	0.82[ASN][1000 genomes]
rs2272338	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2285886	1.00[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2293481	0.93[ASN][1000 genomes]
rs34161112	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35058708	0.87[ASN][1000 genomes]
rs35414630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3807479	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4134888	0.81[ASN][1000 genomes]
rs4134917	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4134923	0.88[ASN][1000 genomes]
rs4729567	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4729568	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4729571	0.83[ASN][1000 genomes]
rs4729572	0.81[ASN][1000 genomes]
rs4729577	1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs62485010	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62485013	0.94[ASN][1000 genomes]
rs6960432	1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6975031	0.85[TSI][hapmap]
rs9649220	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs999886	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs941290	AP4M1	cis	multi-tissue	Pritchard
rs941290	AP4M1	cis	Artery Tibial	GTEx
rs941290	AP4M1	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99677600-99680400	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr7:99677800-99678800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr7:99677800-99679000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr7:99677800-99679000	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr7:99677800-99680600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr7:99678000-99678800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr7:99678000-99678800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
8	chr7:99678000-99679000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr7:99678000-99679000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr7:99678000-99679400	Active TSS	Sigmoid Colon	Sigmoid Colon
11	chr7:99678000-99679400	Active TSS	HSMMtube	muscle
12	chr7:99678000-99679400	Active TSS	NHLF	lung
13	chr7:99678000-99679600	Active TSS	HSMM	muscle
14	chr7:99678000-99679600	Active TSS	NH-A	brain
15	chr7:99678000-99679800	Active TSS	A549	lung
16	chr7:99678000-99680200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr7:99678000-99680400	Active TSS	H1 Cell Line	embryonic stem cell
18	chr7:99678000-99680400	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr7:99678000-99680400	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr7:99678000-99680400	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr7:99678000-99680400	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr7:99678000-99680400	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr7:99678000-99680400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr7:99678000-99680400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr7:99678000-99680400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr7:99678000-99680400	Active TSS	Fetal Kidney	kidney
27	chr7:99678000-99681000	Active TSS	H9 Cell Line	embryonic stem cell
28	chr7:99678200-99678800	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr7:99678200-99678800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr7:99678200-99678800	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr7:99678200-99678800	Flanking Active TSS	Placenta	Placenta
32	chr7:99678200-99679000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr7:99678200-99679000	Flanking Active TSS	Liver	Liver
34	chr7:99678200-99679000	Active TSS	Fetal Brain Female	brain
35	chr7:99678200-99679400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr7:99678200-99679400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr7:99678200-99679400	Active TSS	Muscle Satellite Cultured Cells	--
38	chr7:99678200-99679400	Active TSS	NHDF-Ad	bronchial
39	chr7:99678200-99679600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr7:99678200-99679600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr7:99678200-99679600	Active TSS	NHEK	skin
42	chr7:99678200-99679800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:99678200-99679800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:99678200-99679800	Active TSS	Fetal Intestine Large	intestine
45	chr7:99678200-99679800	Active TSS	Ovary	ovary
46	chr7:99678200-99679800	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr7:99678200-99679800	Active TSS	Hela-S3	cervix
48	chr7:99678200-99679800	Active TSS	HUVEC	blood vessel
49	chr7:99678200-99680000	Active TSS	Colon Smooth Muscle	Colon
50	chr7:99678200-99680200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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