Variant report

Variant	rs345986
Chromosome Location	chr3:156395329-156395330
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:156395327-156396743	Hela-S3	cervix:	n/a	n/a
2	MXI1	chr3:156391527-156396530	IMR90	lung:	n/a	n/a
3	CHD1	chr3:156391341-156402336	IMR90	lung:	n/a	chr3:156392500-156392510
4	POLR2A	chr3:156395031-156396698	A549	lung:	n/a	n/a
5	POLR2A	chr3:156391741-156395648	IMR90	lung:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:156390449..156395705-chr3:156876136..156879645,10	MCF-7	breast:
2	chr3:156394981..156397696-chr3:156877359..156880145,3	MCF-7	breast:
3	chr3:156389452..156396391-chr3:156801976..156809206,19	MCF-7	breast:
4	chr3:156388866..156397270-chr3:156524172..156537549,71	MCF-7	breast:
5	chr3:156391251..156395598-chr3:156875832..156879722,8	K562	blood:
6	chr3:156260735..156275674-chr3:156389736..156397850,44	K562	blood:
7	chr3:156389670..156395497-chr3:156530360..156537244,22	MCF-7	breast:
8	chr3:156390293..156396385-chr3:156542364..156548172,18	MCF-7	breast:
9	chr3:156390535..156395368-chr3:156542467..156546251,7	MCF-7	breast:
10	chr3:156264459..156269953-chr3:156392362..156396309,4	K562	blood:

No data

Variant related genes	Relation type
TIPARP	TF binding region
TIPARP-AS1	TF binding region
ENSG00000230457	Chromatin interaction
ENSG00000240875	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000114850	Chromatin interaction
ENSG00000197980	Chromatin interaction
ENSG00000241135	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12497777	0.83[CHB][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap]
rs13314482	0.91[ASN][1000 genomes]
rs1367311	0.83[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1469536	0.83[TSI][hapmap]
rs168247	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17380702	0.81[CHB][hapmap];0.83[CHD][hapmap]
rs17380954	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs184695	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193197	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs237250	0.86[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs343999	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs344003	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs344018	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344027	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs344028	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs344034	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs344067	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs345985	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs346003	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34901284	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs374341	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs386736	1.00[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap]
rs62277393	0.91[ASN][1000 genomes]
rs62277394	0.91[ASN][1000 genomes]
rs7636965	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9289971	0.83[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs9882795	0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs345986	SMC4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156391600-156395400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:156391600-156395400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:156391600-156395400	Active TSS	Right Atrium	heart
4	chr3:156391600-156395400	Active TSS	Right Ventricle	heart
5	chr3:156391600-156395400	Active TSS	GM12878-XiMat	blood
6	chr3:156391600-156395600	Active TSS	HSMMtube	muscle
7	chr3:156391800-156395400	Active TSS	NHLF	lung
8	chr3:156392000-156395400	Active TSS	HMEC	breast
9	chr3:156393000-156398800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:156393600-156395600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:156393600-156401800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
12	chr3:156393800-156395400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:156393800-156396600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:156394000-156395400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:156394000-156395400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:156394000-156395400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:156394000-156395400	Weak transcription	Small Intestine	intestine
18	chr3:156394000-156395600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:156394000-156395800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:156394000-156395800	Weak transcription	Gastric	stomach
21	chr3:156394000-156395800	Weak transcription	Pancreas	Pancrea
22	chr3:156394000-156395800	Weak transcription	Spleen	Spleen
23	chr3:156394000-156396800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:156394000-156436000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:156394200-156395400	Enhancers	Primary B cells from peripheral blood	blood
26	chr3:156394200-156395400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr3:156394200-156395400	Weak transcription	Stomach Mucosa	stomach
28	chr3:156394200-156395400	Flanking Active TSS	HUVEC	blood vessel
29	chr3:156394200-156395600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:156394200-156395800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr3:156394200-156395800	Weak transcription	Colonic Mucosa	Colon
32	chr3:156394200-156412600	Weak transcription	Placenta	Placenta
33	chr3:156394400-156395400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:156394400-156395400	Enhancers	Brain Substantia Nigra	brain
35	chr3:156394400-156395400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:156394400-156395600	Enhancers	Primary hematopoietic stem cells	blood
37	chr3:156394400-156395600	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr3:156394400-156395600	Enhancers	Brain Cingulate Gyrus	brain
39	chr3:156394400-156395600	Enhancers	Colon Smooth Muscle	Colon
40	chr3:156394400-156395600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:156394400-156395600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:156394400-156395800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr3:156394400-156395800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:156394400-156395800	Weak transcription	Esophagus	oesophagus
45	chr3:156394400-156395800	Weak transcription	Fetal Lung	lung
46	chr3:156394400-156395800	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:156394400-156395800	Weak transcription	Fetal Stomach	stomach
48	chr3:156394400-156395800	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr3:156394400-156398800	Weak transcription	Aorta	Aorta
50	chr3:156394400-156404800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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