Variant report

Variant	rs7630685
Chromosome Location	chr3:48131170-48131171
allele	C/G
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	TCF12	chr3:48130302-48131208	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr3:48130170-48131189	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:48128782-48131544	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:48128789-48131239	SK-N-MC	brain:	n/a	n/a
5	EP300	chr3:48130140-48132020	K562	blood:	n/a	chr3:48130158-48130167 chr3:48130265-48130274 chr3:48130754-48130770
6	MYC	chr3:48130099-48131434	K562	blood:	n/a	n/a
7	PML	chr3:48129973-48131205	GM12878	blood:	n/a	n/a
8	UBTF	chr3:48128928-48131625	K562	blood:	n/a	n/a
9	MAX	chr3:48130105-48131193	A549	lung:	n/a	n/a
10	POLR2A	chr3:48130060-48131192	MCF-7	breast:	n/a	n/a
11	SIN3AK20	chr3:48130086-48131192	MCF-7	breast:	n/a	n/a
12	PML	chr3:48130099-48131173	K562	blood:	n/a	n/a
13	POLR2A	chr3:48129076-48131466	K562	blood:	n/a	n/a
14	POLR2A	chr3:48129856-48131206	PFSK-1	brain:	n/a	n/a
15	ZNF384	chr3:48130229-48131257	K562	blood:	n/a	n/a
16	E2F6	chr3:48130436-48131170	A549	lung:	n/a	chr3:48130853-48130864
17	MAX	chr3:48130091-48131238	ECC-1	luminal epithelium:	n/a	chr3:48130096-48130106
18	POLR2A	chr3:48128760-48131253	MCF10A-Er-Src	breast:	n/a	n/a
19	GTF3C2	chr3:48130065-48131461	K562	blood:	n/a	n/a
20	POLR2A	chr3:48128918-48131220	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:48130087-48131183	HUVEC	blood vessel:	n/a	n/a
22	MAX	chr3:48128639-48131266	K562	blood:	n/a	chr3:48130084-48130094 chr3:48128855-48128865 chr3:48130096-48130106 chr3:48129103-48129112
23	MAX	chr3:48129918-48131191	ECC-1	luminal epithelium:	n/a	chr3:48130084-48130094 chr3:48130096-48130106
24	POLR2A	chr3:48128814-48131226	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr3:48128150-48131439	IMR90	lung:	n/a	n/a
26	MAX	chr3:48128688-48131301	HCT-116	colon:	n/a	chr3:48130084-48130094 chr3:48128855-48128865 chr3:48130096-48130106 chr3:48129103-48129112
27	POLR2A	chr3:48130127-48131172	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr3:48129987-48131189	HL-60	blood:	n/a	n/a
29	SMARCB1	chr3:48129677-48131194	Hela-S3	cervix:	n/a	n/a
30	MXI1	chr3:48128150-48131204	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr3:48129678-48131218	MCF-7	breast:	n/a	n/a
32	POLR2A	chr3:48129596-48131209	HUVEC	blood vessel:	n/a	n/a
33	REST	chr3:48128684-48131251	H1-neurons	neurons:	n/a	chr3:48130295-48130308 chr3:48130081-48130091
34	MYC	chr3:48130320-48131262	MCF10A-Er-Src	breast:	n/a	n/a
35	MAX	chr3:48130263-48131179	A549	lung:	n/a	n/a
36	IRF1	chr3:48130231-48131419	K562	blood:	n/a	chr3:48130372-48130386 chr3:48131386-48131399 chr3:48130800-48130814 chr3:48131386-48131400 chr3:48131388-48131402 chr3:48131385-48131399
37	MYC	chr3:48128727-48131236	K562	blood:	n/a	chr3:48130084-48130094 chr3:48128855-48128865 chr3:48130096-48130106 chr3:48129103-48129112
38	POLR2A	chr3:48128866-48131201	GM12892	blood:	n/a	n/a
39	E2F6	chr3:48130269-48131282	H1-hESC	embryonic stem cell:	n/a	chr3:48130853-48130864
40	POLR2A	chr3:48130082-48131198	MCF-7	breast:	n/a	n/a
41	POLR2A	chr3:48129481-48131445	K562	blood:	n/a	n/a
42	POLR2A	chr3:48129933-48131221	U87	brain:	n/a	n/a
43	TBL1XR1	chr3:48130102-48131832	K562	blood:	n/a	n/a
44	POLR2A	chr3:48128654-48131220	U87	brain:	n/a	n/a
45	POLR2A	chr3:48130119-48131170	GM12878	blood:	n/a	n/a
46	TAF1	chr3:48130007-48131178	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr3:48130004-48131183	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr3:48129078-48131269	Hela-S3	cervix:	n/a	n/a
49	TBP	chr3:48130122-48131272	K562	blood:	n/a	n/a
50	MAX	chr3:48129931-48131192	HCT-116	colon:	n/a	chr3:48130084-48130094 chr3:48130096-48130106

No.	Distal block	Cell Line	Cell type
1	chr3:48130893..48133841-chr3:48154652..48156153,2	K562	blood:
2	chr14:105200530..105201030-chr3:48130853..48131356,2	NB4	blood:
3	chr3:48129047..48133145-chr3:48133622..48137667,6	K562	blood:
4	chr3:48130350..48131236-chr9:124132115..124132795,2	Hela-S3	cervix:
5	chr3:48055864..48058624-chr3:48128858..48131357,3	MCF-7	breast:
6	chr3:48129047..48133145-chr3:48133826..48138274,6	K562	blood:
7	chr3:48129161..48131606-chr3:48228200..48230674,2	MCF-7	breast:
8	chr3:47864865..47866925-chr3:48129196..48131775,2	MCF-7	breast:
9	chr3:47843334..47845793-chr3:48129706..48132338,2	K562	blood:
10	chr3:47843334..47845793-chr3:48129178..48132338,3	K562	blood:
11	chr3:48054963..48058951-chr3:48128022..48131548,4	MCF-7	breast:

Variant related genes	Relation type
MAP4	TF binding region
ENSG00000047849	Chromatin interaction
ENSG00000132153	Chromatin interaction
ENSG00000265078	Chromatin interaction
ENSG00000164045	Chromatin interaction
ENSG00000148175	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs4858882	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS 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	42 gene(s)	inside rSNPs	diseases
2	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' 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	45 gene(s)	inside rSNPs	diseases
5	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv1012828	chr3:47996472-48192862	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv876760	chr3:48019258-48197614	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv834681	chr3:48032000-48181775	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv1012024	chr3:48119229-48242670	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7630685	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs7630685	MRPS18AP1	cis	Nerve Tibial	GTEx
rs7630685	DHX30	Cis_1M	lymphoblastoid	RTeQTL
rs7630685	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs7630685	ZNF589	cis	Nerve Tibial	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48127800-48131200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:48128200-48131200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:48128200-48131600	Active TSS	A549	lung
4	chr3:48128400-48131200	Active TSS	Aorta	Aorta
5	chr3:48128400-48131200	Active TSS	Right Ventricle	heart
6	chr3:48128600-48131200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:48128600-48131200	Active TSS	Psoas Muscle	Psoas
8	chr3:48128800-48131200	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr3:48128800-48131200	Active TSS	Colonic Mucosa	Colon
10	chr3:48128800-48131200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr3:48128800-48131200	Active TSS	HSMMtube	muscle
12	chr3:48128800-48131400	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr3:48128800-48131400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:48128800-48131400	Active TSS	HSMM	muscle
15	chr3:48128800-48131400	Active TSS	NHDF-Ad	bronchial
16	chr3:48128800-48131600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:48128800-48131600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:48128800-48131600	Active TSS	Stomach Smooth Muscle	stomach
19	chr3:48129000-48131200	Active TSS	H9 Cell Line	embryonic stem cell
20	chr3:48129000-48131200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:48129000-48131200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:48129000-48131200	Active TSS	Brain Angular Gyrus	brain
23	chr3:48129000-48131200	Active TSS	Brain Cingulate Gyrus	brain
24	chr3:48129000-48131200	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr3:48129000-48131400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr3:48129000-48131400	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr3:48129000-48131400	Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr3:48129000-48131400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:48129000-48131400	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr3:48129000-48131400	Active TSS	Fetal Kidney	kidney
31	chr3:48129000-48131400	Active TSS	HMEC	breast
32	chr3:48129000-48131400	Active TSS	NHEK	skin
33	chr3:48129000-48131400	Active TSS	NHLF	lung
34	chr3:48129000-48131600	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr3:48129000-48131600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:48129000-48131600	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr3:48129200-48131200	Active TSS	H1 Cell Line	embryonic stem cell
38	chr3:48129200-48131200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr3:48129200-48131200	Active TSS	Brain Hippocampus Middle	brain
40	chr3:48129200-48131200	Active TSS	Brain Substantia Nigra	brain
41	chr3:48129200-48131200	Active TSS	Duodenum Mucosa	Duodenum
42	chr3:48129200-48131400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:48129200-48131400	Active TSS	Thymus	Thymus
44	chr3:48129200-48131400	Active TSS	K562	blood
45	chr3:48129400-48131200	Active TSS	Brain Anterior Caudate	brain
46	chr3:48129400-48131400	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr3:48129400-48131600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:48129600-48131200	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr3:48129600-48131200	Active TSS	Fetal Intestine Large	intestine
50	chr3:48129600-48131200	Active TSS	Rectal Mucosa Donor 31	rectum

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