Variant report

Variant	rs7643913
Chromosome Location	chr3:52303213-52303214
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52303212-52303262	HNPCEpiC	eye:	n/a
2	chr3:52303212-52303262	NB4	blood:	n/a
3	chr3:52303212-52303262	PrEC	prostate:	n/a
4	chr3:52303212-52303262	HEEpiC	esophagus:	n/a
5	chr3:52303212-52303262	ovcar-3	ovarian:	n/a
6	chr3:52303212-52303262	Caco-2	colon:	n/a
7	chr3:52303212-52303262	RPTEC	kidney:	n/a
8	chr3:52303212-52303262	HRPEpiC	eye:	n/a
9	chr3:52303212-52303262	K562	blood:	n/a
10	chr3:52303212-52303262	T-47D	breast:	n/a
11	chr3:52303212-52303262	HEK293	kidney:	embryo
12	chr3:52303212-52303262	H1-hESC	embryonic stem cell:	embryo
13	chr3:52303212-52303262	LNCaP	prostate:	n/a
14	chr3:52303212-52303262	AG04449	skin:	fetal
15	chr3:52303212-52303262	MCF-7	breast:	n/a
16	chr3:52303212-52303262	PFSK-1	brain:	n/a
17	chr3:52303212-52303262	HMEC	breast:	n/a
18	chr3:52303212-52303262	IMR90	lung:	fetal
19	chr3:52303212-52303262	SK-N-SH	brain:	n/a
20	chr3:52303212-52303262	CMK	blood:	n/a
21	chr3:52303212-52303262	MCF10A-Er-Src	breast:	n/a
22	chr3:52303212-52303262	GM19239	blood:	n/a
23	chr3:52303212-52303262	NHDF-neo	bronchial:	n/a
24	chr3:52303212-52303262	GM12878	blood:	n/a
25	chr3:52303212-52303262	SK-N-MC	brain:	n/a
26	chr3:52303212-52303262	SAEC	small airway:	n/a
27	chr3:52303212-52303262	HCM	heart:	n/a
28	chr3:52303212-52303262	HCT-116	colon:	n/a
29	chr3:52303212-52303262	Hepatocyte	liver:	n/a
30	chr3:52303212-52303262	AG10803	skin:	n/a
31	chr3:52303212-52303262	GM12892	blood:	n/a
32	chr3:52303212-52303262	HRCEpiC	kidney:	n/a
33	chr3:52303212-52303262	BE2_C	brain:	n/a
34	chr3:52303212-52303262	SKMC	muscle:	n/a
35	chr3:52303212-52303262	ECC-1	luminal epithelium:	n/a
36	chr3:52303212-52303262	NH-A	brain:	n/a
37	chr3:52303212-52303262	GM12891	blood:	n/a
38	chr3:52303212-52303262	Jurkat	blood:	n/a
39	chr3:52303212-52303262	AG09319	gingival:	n/a
40	chr3:52303212-52303262	HCPEpiC	choroid plexus:	n/a
41	chr3:52303212-52303262	HepG2	liver:	n/a
42	chr3:52303212-52303262	Hela-S3	cervix:	n/a
43	chr3:52303212-52303262	A549	lung:	n/a
44	chr3:52303212-52303262	NHBE	bronchial:	n/a
45	chr3:52303212-52303262	U87	brain:	n/a
46	chr3:52303212-52303262	NT2-D1	testis:	n/a
47	chr3:52303212-52303262	HUVEC	blood vessel:	n/a
48	chr3:52303212-52303262	ProgFib	skin:	n/a
49	chr3:52303212-52303262	PANC-1	pancreas:	n/a
50	chr3:52303212-52303262	SK-N-SH_RA	brain:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52271620..52273197-chr3:52302403..52304175,2	MCF-7	breast:
2	chr3:52297780..52305259-chr3:52310132..52314407,14	MCF-7	breast:

No data

Variant related genes	Relation type
MIRLET7G	CpG island
WDR82	CpG island
ENSG00000239732	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000247596	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10460962	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461027	0.86[CEU][hapmap];0.97[EUR][1000 genomes]
rs10461028	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10865971	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs11706515	0.86[CEU][hapmap];0.94[EUR][1000 genomes]
rs11706541	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11707056	0.86[CEU][hapmap];1.00[EUR][1000 genomes]
rs11708581	0.94[EUR][1000 genomes]
rs11708811	0.86[CEU][hapmap];1.00[EUR][1000 genomes]
rs11710014	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11711914	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11711974	0.86[CEU][hapmap];0.94[EUR][1000 genomes]
rs11713464	0.89[AMR][1000 genomes]
rs11713914	0.86[CEU][hapmap];0.94[EUR][1000 genomes]
rs11714313	0.82[AMR][1000 genomes]
rs11714358	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11715208	1.00[EUR][1000 genomes]
rs11715382	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11715391	0.86[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11716487	0.86[CEU][hapmap]
rs11717028	0.97[EUR][1000 genomes]
rs11717574	0.82[AMR][1000 genomes]
rs11718729	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11719760	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11720365	0.86[CEU][hapmap];0.94[EUR][1000 genomes]
rs11721277	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17052051	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17052052	0.86[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17052053	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17052054	0.86[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17263770	0.81[EUR][1000 genomes]
rs1767	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1769	1.00[CEU][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35976326	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3733063	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3852062	0.82[AMR][1000 genomes]
rs3886875	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs4082828	0.86[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55676974	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55806905	0.94[EUR][1000 genomes]
rs55813842	0.94[EUR][1000 genomes]
rs55847657	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56002041	0.94[EUR][1000 genomes]
rs56322342	0.94[EUR][1000 genomes]
rs56352611	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56899118	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57849650	0.94[EUR][1000 genomes]
rs58531656	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58879205	0.89[AMR][1000 genomes]
rs60382084	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61644644	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445385	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6776759	0.81[EUR][1000 genomes]
rs6783652	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6793317	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6809248	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs724801	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs729555	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs73072990	0.88[EUR][1000 genomes]
rs73088773	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73088783	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088785	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088791	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73088800	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73091166	0.94[EUR][1000 genomes]
rs73091168	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs746239	0.94[EUR][1000 genomes]
rs7615405	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7628461	0.86[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7633687	0.86[CEU][hapmap];0.94[EUR][1000 genomes]
rs7638204	0.86[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
5	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
6	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
7	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS 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	117 gene(s)	inside rSNPs	diseases
8	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
9	nsv822090	chr3:52292814-52311153	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7643913	PPM1M	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52281800-52303400	Weak transcription	Right Atrium	heart
2	chr3:52282200-52310000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:52282400-52309600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:52282600-52304000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:52282600-52308200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:52282800-52303800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:52282800-52305000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:52283000-52306000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:52283200-52308400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:52283400-52304600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:52283400-52305400	Strong transcription	Brain Germinal Matrix	brain
12	chr3:52283600-52308800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr3:52283800-52309600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:52284400-52304800	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:52284600-52305800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:52285600-52308400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:52285800-52307400	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr3:52286400-52306800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:52286600-52303400	Strong transcription	NHLF	lung
20	chr3:52287400-52305400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:52287400-52305600	Strong transcription	HepG2	liver
22	chr3:52288000-52303400	Strong transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:52288000-52304200	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr3:52288000-52304200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr3:52288000-52304400	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr3:52288000-52305000	Strong transcription	Fetal Brain Female	brain
27	chr3:52288000-52305800	Strong transcription	Fetal Muscle Leg	muscle
28	chr3:52288200-52303400	Strong transcription	Colonic Mucosa	Colon
29	chr3:52288200-52303600	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:52288400-52303400	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:52288400-52304000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr3:52288400-52304000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr3:52288400-52304200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr3:52288400-52304200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:52288400-52304800	Strong transcription	Fetal Stomach	stomach
36	chr3:52288800-52303400	Strong transcription	Primary hematopoietic stem cells	blood
37	chr3:52288800-52304400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr3:52289000-52303400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:52289400-52303600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:52289600-52303600	Strong transcription	Rectal Smooth Muscle	rectum
41	chr3:52289800-52303400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:52290400-52305000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:52291400-52304800	Strong transcription	Thymus	Thymus
44	chr3:52292400-52309400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:52292800-52305800	Strong transcription	Fetal Intestine Large	intestine
46	chr3:52293000-52308000	Weak transcription	Stomach Mucosa	stomach
47	chr3:52293400-52304400	Strong transcription	Osteobl	bone
48	chr3:52293400-52304800	Strong transcription	Dnd41	blood
49	chr3:52293600-52303400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:52293600-52304800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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