Variant report

Variant	rs4679895
Chromosome Location	chr3:160285898-160285899
allele	C/T
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	POLR2A	chr3:160285880-160286136	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:160285826-160286040	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:160285787-160285905	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:160165891..160168986-chr3:160283501..160286413,4	K562	blood:
2	chr3:160281906..160285341-chr3:160285654..160289811,8	MCF-7	breast:
3	chr3:160282613..160284767-chr3:160285868..160288833,4	MCF-7	breast:
4	chr3:160165801..160167391-chr3:160284829..160286413,2	K562	blood:

Variant related genes	Relation type
KPNA4	TF binding region
ENSG00000213186	Chromatin interaction
ENSG00000186432	Chromatin interaction
ENSG00000229320	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1369666	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17570467	0.81[AMR][1000 genomes]
rs1882126	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1920649	0.87[ASN][1000 genomes]
rs1920652	0.87[ASN][1000 genomes]
rs1920659	0.86[ASN][1000 genomes]
rs1971128	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2123003	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3732706	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732707	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3851365	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4292273	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4292274	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4679654	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4679655	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4679896	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4679900	0.80[ASN][1000 genomes]
rs4680589	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680591	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56156703	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62272810	0.80[ASN][1000 genomes]
rs6806505	0.80[ASN][1000 genomes]
rs7644453	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7648393	0.86[ASN][1000 genomes]
rs9816525	0.87[ASN][1000 genomes]
rs9822982	0.87[ASN][1000 genomes]
rs9857106	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
5	nsv877702	chr3:160262803-160304614	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
6	nsv4089	chr3:160284848-160330024	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv963373	chr3:160285741-160287108	ZNF genes & repeats Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4679895	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160284200-160286200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:160284200-160286400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:160284200-160289600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:160284400-160286200	Weak transcription	Pancreas	Pancrea
5	chr3:160284400-160286600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr3:160284400-160286800	Weak transcription	Fetal Thymus	thymus
7	chr3:160284600-160286200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr3:160284600-160286200	Weak transcription	Left Ventricle	heart
9	chr3:160284600-160286400	Weak transcription	Aorta	Aorta
10	chr3:160284600-160286400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:160284600-160286800	Weak transcription	Thymus	Thymus
12	chr3:160284600-160287000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:160284600-160288400	Weak transcription	Ovary	ovary
14	chr3:160284800-160287200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr3:160284800-160287200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:160284800-160287600	Weak transcription	Fetal Intestine Large	intestine
17	chr3:160284800-160287800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr3:160284800-160288200	Weak transcription	Brain Substantia Nigra	brain
19	chr3:160284800-160288400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:160284800-160289600	Weak transcription	Fetal Lung	lung
21	chr3:160284800-160292000	Weak transcription	Brain Anterior Caudate	brain
22	chr3:160284800-160295000	Weak transcription	Stomach Mucosa	stomach
23	chr3:160284800-160295200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:160285000-160286000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:160285000-160286000	Weak transcription	Adipose Nuclei	Adipose
26	chr3:160285000-160287000	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:160285000-160287200	Weak transcription	GM12878-XiMat	blood
28	chr3:160285000-160287400	Enhancers	Dnd41	blood
29	chr3:160285000-160287800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:160285000-160287800	Weak transcription	Liver	Liver
31	chr3:160285000-160289600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:160285000-160290800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr3:160285000-160292200	Weak transcription	Primary B cells from cord blood	blood
34	chr3:160285200-160286000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:160285200-160286000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:160285200-160286200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:160285200-160286200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:160285200-160286200	Weak transcription	A549	lung
39	chr3:160285200-160286200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr3:160285200-160287000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:160285200-160287600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr3:160285200-160287600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:160285200-160287800	Weak transcription	Psoas Muscle	Psoas
44	chr3:160285200-160288000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:160285200-160289600	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:160285200-160293400	Weak transcription	HepG2	liver
47	chr3:160285200-160294400	Weak transcription	HSMMtube	muscle
48	chr3:160285200-160298800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:160285400-160286000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:160285400-160286000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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