Variant report

Variant	rs9843737
Chromosome Location	chr3:160116174-160116175
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:160116103-160120669	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:160116172-160118593	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:160116133-160118512	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160024329..160027233-chr3:160115797..160118305,2	K562	blood:
2	chr3:159943099..159944633-chr3:160116148..160118841,2	K562	blood:
3	chr3:160116116..160127665-chr3:160158037..160169627,42	K562	blood:
4	chr3:160116021..160118602-chr3:179040566..179042306,2	K562	blood:
5	chr3:160011686..160013394-chr3:160115179..160116949,3	MCF-7	breast:
6	chr3:160116116..160124648-chr3:160162504..160168767,20	K562	blood:
7	chr3:160115701..160119261-chr3:160281379..160284712,4	MCF-7	breast:

No data

Variant related genes	Relation type
SMC4	TF binding region
ENSG00000180044	Chromatin interaction
ENSG00000244078	Chromatin interaction
ENSG00000213186	Chromatin interaction
ENSG00000229320	Chromatin interaction
ENSG00000121864	Chromatin interaction
ENSG00000186432	Chromatin interaction
ENSG00000068885	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10212356	1.00[CEU][hapmap]
rs11919703	0.86[EUR][1000 genomes]
rs13314803	0.86[EUR][1000 genomes]
rs16831131	1.00[MEX][hapmap]
rs1920661	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap]
rs28599984	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2886772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4274790	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6764829	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73875246	0.87[AMR][1000 genomes]
rs9812738	1.00[CHD][hapmap]
rs9813697	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9829578	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9845395	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9874550	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9879379	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
7	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
8	esv1795255	chr3:160089896-160153305	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	205 gene(s)	inside rSNPs	diseases
9	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases
10	nsv963540	chr3:160113220-160120396	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160076200-160116200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:160088800-160116200	Weak transcription	Primary B cells from cord blood	blood
3	chr3:160088800-160116200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr3:160092200-160116200	Weak transcription	Fetal Intestine Small	intestine
5	chr3:160092200-160116600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:160094800-160116600	Weak transcription	Left Ventricle	heart
7	chr3:160098400-160116200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:160098400-160116400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:160098800-160116200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:160109000-160116200	Weak transcription	Stomach Mucosa	stomach
11	chr3:160110800-160116200	Weak transcription	Psoas Muscle	Psoas
12	chr3:160111800-160116200	Enhancers	Primary T cells from cord blood	blood
13	chr3:160113600-160116200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:160113600-160116200	Weak transcription	HSMM	muscle
15	chr3:160114600-160121800	Active TSS	GM12878-XiMat	blood
16	chr3:160115000-160116200	Enhancers	Fetal Lung	lung
17	chr3:160115200-160116200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:160115200-160116400	Enhancers	Fetal Heart	heart
19	chr3:160115200-160120600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:160115600-160116200	Enhancers	Primary T cells fromperipheralblood	blood
21	chr3:160115600-160116200	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr3:160115800-160116200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr3:160115800-160116200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:160115800-160116200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:160115800-160116200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:160115800-160116200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr3:160115800-160116200	Enhancers	Brain Cingulate Gyrus	brain
28	chr3:160115800-160116200	Enhancers	Fetal Intestine Large	intestine
29	chr3:160115800-160116400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:160115800-160116600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:160115800-160116600	Flanking Active TSS	Dnd41	blood
32	chr3:160115800-160116600	Flanking Active TSS	NHEK	skin
33	chr3:160115800-160116800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:160115800-160120000	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr3:160116000-160116200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr3:160116000-160116200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr3:160116000-160116200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:160116000-160116200	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr3:160116000-160116200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr3:160116000-160116200	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr3:160116000-160116200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:160116000-160116200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr3:160116000-160116200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:160116000-160116200	Enhancers	Adipose Nuclei	Adipose
45	chr3:160116000-160116200	Enhancers	Brain Angular Gyrus	brain
46	chr3:160116000-160116200	Enhancers	Brain Anterior Caudate	brain
47	chr3:160116000-160116200	Enhancers	Brain Germinal Matrix	brain
48	chr3:160116000-160116200	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr3:160116000-160116200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:160116000-160116200	Enhancers	Colon Smooth Muscle	Colon

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