Variant report

Variant	rs12878
Chromosome Location	chr7:99747130-99747131
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:98)
CpG islands
(count:61)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:98 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr7:99745989-99747150	H1-hESC	embryonic stem cell:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
2	PBX3	chr7:99745890-99747320	SK-N-SH	brain:	n/a	chr7:99746470-99746490
3	POLR2A	chr7:99745576-99747499	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr7:99747119-99747199	HepG2	liver:	n/a	n/a
5	STAT1	chr7:99747128-99747265	GM12878	blood:	n/a	n/a
6	WRNIP1	chr7:99747021-99747258	GM12878	blood:	n/a	n/a
7	MAX	chr7:99745870-99747362	MCF-7	breast:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
8	HCFC1	chr7:99745930-99747565	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr7:99745829-99747396	GM12878	blood:	n/a	n/a
10	MAX	chr7:99745811-99747316	A549	lung:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
11	CHD2	chr7:99746128-99747167	Hela-S3	cervix:	n/a	chr7:99746351-99746361
12	POLR2A	chr7:99746032-99747255	A549	lung:	n/a	n/a
13	POLR2A	chr7:99745584-99747320	HepG2	liver:	n/a	n/a
14	POLR2A	chr7:99745874-99747324	K562	blood:	n/a	n/a
15	HMGN3	chr7:99746114-99747154	K562	blood:	n/a	n/a
16	POLR2A	chr7:99745935-99747236	GM12892	blood:	n/a	n/a
17	MAZ	chr7:99747045-99747194	Hela-S3	cervix:	n/a	n/a
18	ZEB1	chr7:99747037-99747261	GM12878	blood:	n/a	n/a
19	ZBTB7A	chr7:99746466-99747297	K562	blood:	n/a	n/a
20	POLR2A	chr7:99745934-99747370	H1-hESC	embryonic stem cell:	n/a	n/a
21	ZNF143	chr7:99747032-99747210	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr7:99745994-99747324	H1-neurons	neurons:	n/a	n/a
23	POLR2A	chr7:99746051-99747163	Hela-S3	cervix:	n/a	n/a
24	SIN3A	chr7:99746220-99747203	H1-hESC	embryonic stem cell:	n/a	n/a
25	MYC	chr7:99746111-99747222	K562	blood:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
26	POLR2A	chr7:99745814-99747302	K562	blood:	n/a	n/a
27	POLR2A	chr7:99746004-99747250	GM19099	blood:	n/a	n/a
28	POLR2A	chr7:99746981-99747239	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr7:99747014-99747248	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr7:99746072-99747174	MCF10A-Er-Src	breast:	n/a	n/a
31	JUN	chr7:99745805-99747561	K562	blood:	n/a	chr7:99746137-99746146
32	MAX	chr7:99746863-99747320	K562	blood:	n/a	n/a
33	MXI1	chr7:99745662-99747561	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr7:99747103-99747343	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr7:99746007-99747266	GM19193	blood:	n/a	n/a
36	POLR2A	chr7:99745804-99747481	GM12891	blood:	n/a	n/a
37	NFATC1	chr7:99746841-99747209	GM12878	blood:	n/a	n/a
38	POLR2A	chr7:99745940-99747216	GM12878	blood:	n/a	n/a
39	MAZ	chr7:99746030-99747312	K562	blood:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
40	NR2F2	chr7:99745801-99747458	K562	blood:	n/a	n/a
41	MAX	chr7:99746186-99747134	Hela-S3	cervix:	n/a	chr7:99746525-99746534
42	MTA3	chr7:99745812-99747487	GM12878	blood:	n/a	n/a
43	POLR2A	chr7:99745915-99747210	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr7:99746959-99747224	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr7:99745971-99747302	MCF-7	breast:	n/a	n/a
46	POLR2A	chr7:99745973-99747381	H1-neurons	neurons:	n/a	n/a
47	POLR2A	chr7:99745963-99747303	ECC-1	luminal epithelium:	n/a	n/a
48	MYC	chr7:99747040-99747160	K562	blood:	n/a	n/a
49	MAZ	chr7:99745857-99747393	IMR90	lung:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
50	POLR2A	chr7:99745856-99747302	U87	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:99747129-99747179	PFSK-1	brain:	n/a
2	chr7:99747129-99747179	HRE	kidney:	n/a
3	chr7:99747129-99747179	PrEC	prostate:	n/a
4	chr7:99747129-99747179	NB4	blood:	n/a
5	chr7:99747129-99747179	HMEC	breast:	n/a
6	chr7:99747129-99747179	HepG2	liver:	n/a
7	chr7:99747129-99747179	GM12892	blood:	n/a
8	chr7:99747129-99747179	HIPEpiC	eye:	n/a
9	chr7:99747129-99747179	Hela-S3	cervix:	n/a
10	chr7:99747129-99747179	NT2-D1	testis:	n/a
11	chr7:99747129-99747179	IMR90	lung:	fetal
12	chr7:99747129-99747179	BJ	skin:	n/a
13	chr7:99747129-99747179	LNCaP	prostate:	n/a
14	chr7:99747129-99747179	AG04450	lung:	fetal
15	chr7:99747129-99747179	PANC-1	pancreas:	n/a
16	chr7:99747129-99747179	AG04449	skin:	fetal
17	chr7:99747129-99747179	SK-N-MC	brain:	n/a
18	chr7:99747129-99747179	GM12891	blood:	n/a
19	chr7:99747129-99747179	AG09319	gingival:	n/a
20	chr7:99747129-99747179	HCPEpiC	choroid plexus:	n/a
21	chr7:99747129-99747179	Caco-2	colon:	n/a
22	chr7:99747129-99747179	SK-N-SH	brain:	n/a
23	chr7:99747129-99747179	NHBE	bronchial:	n/a
24	chr7:99747129-99747179	ovcar-3	ovarian:	n/a
25	chr7:99747129-99747179	HCT-116	colon:	n/a
26	chr7:99747129-99747179	ProgFib	skin:	n/a
27	chr7:99747129-99747179	MCF10A-Er-Src	breast:	n/a
28	chr7:99747129-99747179	HEK293	kidney:	embryo
29	chr7:99747129-99747179	HRCEpiC	kidney:	n/a
30	chr7:99747129-99747179	GM12878	blood:	n/a
31	chr7:99747129-99747179	HL-60	blood:	n/a
32	chr7:99747129-99747179	SAEC	small airway:	n/a
33	chr7:99747129-99747179	GM19239	blood:	n/a
34	chr7:99747129-99747179	RPTEC	kidney:	n/a
35	chr7:99747129-99747179	U87	brain:	n/a
36	chr7:99747129-99747179	AoSMC	blood vessel:	n/a
37	chr7:99747129-99747179	AG09309	skin:	n/a
38	chr7:99747129-99747179	HCM	heart:	n/a
39	chr7:99747129-99747179	HCF	heart:	n/a
40	chr7:99747129-99747179	HAEpiC	amniotic membrane:	n/a
41	chr7:99747129-99747179	HEEpiC	esophagus:	n/a
42	chr7:99747129-99747179	Jurkat	blood:	n/a
43	chr7:99747129-99747179	HRPEpiC	eye:	n/a
44	chr7:99747129-99747179	HPAEpiC	pulmonary alveolar:	n/a
45	chr7:99747129-99747179	BE2_C	brain:	n/a
46	chr7:99747129-99747179	SK-N-SH_RA	brain:	n/a
47	chr7:99747129-99747179	K562	blood:	n/a
48	chr7:99747129-99747179	T-47D	breast:	n/a
49	chr7:99747129-99747179	ECC-1	luminal epithelium:	n/a
50	chr7:99747129-99747179	HUVEC	blood vessel:	n/a

(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
LAMTOR4	CpG island
ENSG00000066923	Chromatin interaction
ENSG00000106290	Chromatin interaction
ENSG00000214142	Chromatin interaction
ENSG00000214309	Chromatin interaction
ENSG00000166508	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000166526	Chromatin interaction
ENSG00000221838	Chromatin interaction
ENSG00000166997	Chromatin interaction
ENSG00000239521	Chromatin interaction
ENSG00000242798	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000160844	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10231604	0.88[GIH][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11764584	0.88[GIH][hapmap];0.88[MEX][hapmap];0.83[ASN][1000 genomes]
rs13309	0.83[CEU][hapmap]
rs1918353	0.84[GIH][hapmap]
rs2272337	0.88[GIH][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.83[YRI][hapmap];0.82[ASN][1000 genomes]
rs2272338	0.94[ASW][hapmap];0.84[CEU][hapmap];0.93[LWK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap]
rs2405440	0.83[YRI][hapmap]
rs35042434	0.82[ASN][1000 genomes]
rs3736590	0.88[GIH][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs3736591	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3779047	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3800951	0.88[GIH][hapmap];0.88[MEX][hapmap]
rs3807479	0.83[CEU][hapmap];0.96[YRI][hapmap]
rs3823646	0.88[GIH][hapmap];0.88[MEX][hapmap]
rs4134917	0.94[ASW][hapmap];0.84[CEU][hapmap];0.88[GIH][hapmap];0.93[LWK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap]
rs4729567	0.84[CEU][hapmap]
rs4729568	0.84[ASW][hapmap];0.84[CEU][hapmap];0.96[YRI][hapmap]
rs4729577	0.94[ASW][hapmap];0.84[CEU][hapmap];0.91[LWK][hapmap];0.82[TSI][hapmap];0.96[YRI][hapmap]
rs6960432	0.84[CEU][hapmap];0.93[YRI][hapmap]
rs7785392	0.88[GIH][hapmap];0.92[MEX][hapmap];0.84[ASN][1000 genomes]
rs9649220	0.84[ASW][hapmap];0.84[CEU][hapmap];0.96[YRI][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12878	AP4M1	cis	cerebellum	SCAN
rs12878	ZKSCAN1	cis	multi-tissue	Pritchard
rs12878	AP4M1	cis	lymphoblastoid	seeQTL
rs12878	MEPCE	cis	frontal cortex	BrainEAC
rs12878	ZSCAN21	cis	parietal	SCAN
rs12878	AP4M1	cis	Artery Tibial	GTEx
rs12878	AP4M1	cis	Esophagus Muscularis	GTEx
rs12878	AP4M1	cis	multi-tissue	Pritchard
rs12878	MBLAC1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99745800-99747200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr7:99745800-99747200	Active TSS	Brain Cingulate Gyrus	brain
3	chr7:99745800-99747200	Active TSS	Brain Hippocampus Middle	brain
4	chr7:99745800-99747400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr7:99745800-99747400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr7:99745800-99747400	Active TSS	Fetal Stomach	stomach
7	chr7:99745800-99747600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr7:99745800-99747600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:99745800-99747600	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr7:99745800-99747800	Active TSS	Fetal Kidney	kidney
11	chr7:99745800-99748200	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr7:99746000-99747200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:99746000-99747200	Active TSS	Aorta	Aorta
14	chr7:99746000-99747200	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr7:99746000-99747200	Active TSS	NHLF	lung
16	chr7:99746000-99747400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr7:99746000-99747400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:99746000-99747400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:99746000-99747400	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr7:99746000-99747400	Active TSS	Esophagus	oesophagus
21	chr7:99746000-99747400	Active TSS	Gastric	stomach
22	chr7:99746000-99747400	Active TSS	Lung	lung
23	chr7:99746000-99747400	Active TSS	Ovary	ovary
24	chr7:99746000-99747400	Active TSS	Pancreas	Pancrea
25	chr7:99746000-99747400	Active TSS	Psoas Muscle	Psoas
26	chr7:99746000-99747400	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr7:99746000-99747600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr7:99746000-99747600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:99746000-99747600	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr7:99746000-99747600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr7:99746000-99747600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
32	chr7:99746000-99747600	Active TSS	NHDF-Ad	bronchial
33	chr7:99746000-99747800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr7:99746000-99748200	Active TSS	A549	lung
35	chr7:99746200-99747200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr7:99746200-99747200	Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr7:99746200-99747200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr7:99746200-99747200	Active TSS	Duodenum Mucosa	Duodenum
39	chr7:99746200-99747200	Active TSS	Fetal Lung	lung
40	chr7:99746200-99747200	Active TSS	Small Intestine	intestine
41	chr7:99746200-99747200	Active TSS	Osteobl	bone
42	chr7:99746200-99747400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr7:99746200-99747400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr7:99746200-99747400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr7:99746200-99747400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr7:99746200-99747400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr7:99746200-99747400	Active TSS	Thymus	Thymus
48	chr7:99746200-99747400	Active TSS	HSMM	muscle
49	chr7:99746200-99747400	Active TSS	HSMMtube	muscle
50	chr7:99746200-99747600	Active TSS	iPS-18 Cell Line	embryonic stem cell

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