Variant report

Variant	rs1534309
Chromosome Location	chr7:99696370-99696371
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99695581-99696441	HL-60	blood:	n/a	n/a
2	POLR2A	chr7:99694417-99699772	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr7:99694796-99696431	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr7:99694703-99697612	GM12892	blood:	n/a	n/a
5	POLR2A	chr7:99695601-99696378	GM12891	blood:	n/a	n/a
6	POLR2A	chr7:99694640-99696904	K562	blood:	n/a	n/a
7	POLR2A	chr7:99694653-99697678	H1-hESC	embryonic stem cell:	n/a	n/a
8	MXI1	chr7:99696123-99700530	SK-N-SH	brain:	n/a	chr7:99696168-99696177 chr7:99699039-99699048
9	HEY1	chr7:99694628-99697652	K562	blood:	n/a	chr7:99695196-99695205
10	POLR2A	chr7:99696030-99697157	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr7:99687998-99697728	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr7:99696321-99696486	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr7:99694683-99696815	K562	blood:	n/a	n/a
14	POLR2A	chr7:99687562-99696983	HepG2	liver:	n/a	n/a
15	POLR2A	chr7:99694702-99697727	K562	blood:	n/a	n/a
16	POLR2A	chr7:99694608-99696959	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr7:99694646-99700079	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr7:99694505-99700789	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr7:99695914-99696437	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr7:99694559-99697007	GM12892	blood:	n/a	n/a
21	POLR2A	chr7:99694635-99697617	K562	blood:	n/a	n/a
22	POLR2A	chr7:99694990-99696427	HL-60	blood:	n/a	n/a
23	POLR2A	chr7:99694572-99696494	K562	blood:	n/a	n/a
24	POLR2A	chr7:99694689-99697009	GM12892	blood:	n/a	n/a
25	POLR2A	chr7:99694793-99696820	K562	blood:	n/a	n/a
26	POLR2A	chr7:99694594-99699682	GM12878	blood:	n/a	n/a
27	POLR2A	chr7:99694577-99700301	SK-N-MC	brain:	n/a	n/a
28	POLR2A	chr7:99696355-99697688	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99696160..99700887-chr7:99753963..99757907,5	K562	blood:
2	chr7:99695452..99699124-chr7:100025277..100027831,3	MCF-7	breast:
3	chr7:99696160..99699295-chr7:99753963..99757907,4	K562	blood:
4	chr7:99645952..99651427-chr7:99695296..99699701,5	K562	blood:
5	chr7:99696142..99700081-chr7:99754300..99760427,7	MCF-7	breast:
6	chr17:56734803..56736757-chr7:99696174..99697894,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR106B	TF binding region
AP4M1	TF binding region
MCM7	TF binding region
MIR93	TF binding region
ENSG00000146826	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000266154	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000166529	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1050542	0.84[ASN][1000 genomes]
rs1141057	0.87[ASN][1000 genomes]
rs11550034	1.00[CHB][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]
rs1569055	0.82[ASN][1000 genomes]
rs2272338	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2285886	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2293481	0.93[ASN][1000 genomes]
rs34161112	0.90[ASN][1000 genomes]
rs35058708	0.87[ASN][1000 genomes]
rs35414630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs3807479	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4134888	0.81[ASN][1000 genomes]
rs4134917	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4134923	0.88[ASN][1000 genomes]
rs4729567	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4729568	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4729571	0.83[ASN][1000 genomes]
rs4729572	0.81[ASN][1000 genomes]
rs4729577	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs62485010	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62485013	0.94[ASN][1000 genomes]
rs6960432	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs941290	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]
rs9649220	1.00[JPT][hapmap]
rs999886	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1534309	AP4M1	cis	multi-tissue	Pritchard
rs1534309	AP4M1	cis	Artery Tibial	GTEx
rs1534309	AP4M1	cis	Lymphoblastoid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99687400-99697200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:99687600-99696600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr7:99687600-99696800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:99687800-99696600	Strong transcription	Fetal Intestine Small	intestine
5	chr7:99688000-99696400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr7:99688000-99696400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr7:99688000-99696400	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr7:99688000-99696400	Strong transcription	Thymus	Thymus
9	chr7:99688000-99696600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:99688000-99696600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:99688000-99696600	Strong transcription	Primary hematopoietic stem cells	blood
12	chr7:99688000-99696600	Strong transcription	Duodenum Mucosa	Duodenum
13	chr7:99688000-99696600	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr7:99688000-99696800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:99688000-99696800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr7:99688000-99696800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr7:99688000-99696800	Strong transcription	Brain Angular Gyrus	brain
18	chr7:99688000-99697000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:99688000-99697000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr7:99688000-99697000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr7:99688000-99697000	Strong transcription	A549	lung
22	chr7:99688000-99697000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr7:99688000-99697200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr7:99688000-99697200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr7:99688000-99697200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:99688000-99697200	Strong transcription	Brain Anterior Caudate	brain
27	chr7:99688000-99697200	Strong transcription	Brain Hippocampus Middle	brain
28	chr7:99688000-99697200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:99688000-99697200	Strong transcription	Left Ventricle	heart
30	chr7:99688000-99697200	Strong transcription	Ovary	ovary
31	chr7:99688000-99697200	Strong transcription	NHEK	skin
32	chr7:99688200-99696400	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr7:99688200-99696600	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr7:99688200-99696600	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr7:99688200-99696600	Strong transcription	Primary B cells from cord blood	blood
36	chr7:99688200-99696600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr7:99688200-99696600	Strong transcription	Gastric	stomach
38	chr7:99688200-99696600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr7:99688200-99696800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr7:99688200-99696800	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr7:99688200-99697000	Strong transcription	Brain Cingulate Gyrus	brain
42	chr7:99688200-99697200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
43	chr7:99688200-99697200	Strong transcription	Brain Substantia Nigra	brain
44	chr7:99688200-99697400	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr7:99688400-99696600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:99688400-99696600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr7:99688400-99696800	Strong transcription	Colonic Mucosa	Colon
48	chr7:99688400-99696800	Strong transcription	Colon Smooth Muscle	Colon
49	chr7:99688600-99696600	Strong transcription	HepG2	liver
50	chr7:99688600-99697400	Strong transcription	Aorta	Aorta

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