Variant report

Variant	rs2705564
Chromosome Location	chr3:112281866-112281867
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr3:112281780-112282527	GM12878	blood:	n/a	n/a
2	MXI1	chr3:112279150-112282285	SK-N-SH	brain:	n/a	n/a
3	PML	chr3:112281777-112282381	GM12878	blood:	n/a	n/a
4	ATF2	chr3:112281815-112282342	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:112279860-112282181	GM18505	blood:	n/a	n/a
6	POLR2A	chr3:112279755-112282233	GM12892	blood:	n/a	n/a
7	GTF3C2	chr3:112280878-112282212	K562	blood:	n/a	n/a
8	JUN	chr3:112281811-112282173	K562	blood:	n/a	n/a
9	POLR2A	chr3:112281797-112282228	GM12892	blood:	n/a	n/a
10	POLR2A	chr3:112281812-112282157	GM12878	blood:	n/a	n/a
11	FOXM1	chr3:112281780-112282318	GM12878	blood:	n/a	n/a
12	NFIC	chr3:112281790-112282276	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:112280025-112281869	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:112279683..112282381-chr3:112710182..112712390,2	K562	blood:
2	chr3:112279172..112282504-chr3:112358640..112361542,6	MCF-7	breast:
3	chr3:112281323..112284151-chr3:113775113..113776995,2	K562	blood:
4	chr3:112279230..112282432-chr3:112358112..112361671,5	K562	blood:
5	chr3:112278745..112284115-chr3:112357887..112361363,11	MCF-7	breast:
6	chr3:112279739..112282135-chr3:112735331..112738696,3	K562	blood:
7	chr3:112280159..112284151-chr3:113775113..113778230,3	K562	blood:
8	chr3:112280777..112282990-chr3:112288928..112291699,3	MCF-7	breast:
9	chr3:112257078..112259281-chr3:112279236..112282506,3	MCF-7	breast:

No data

Variant related genes	Relation type
ATG3	TF binding region
SLC35A5	TF binding region
ENSG00000240057	Chromatin interaction
ENSG00000151576	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000138459	Chromatin interaction
ENSG00000163608	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000163617	Chromatin interaction
ENSG00000163607	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1105938	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1155073	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1488259	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1533159	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1601852	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1814052	0.87[ASN][1000 genomes]
rs1873572	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2171514	0.87[ASN][1000 genomes]
rs2292442	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633574	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2633575	0.87[ASN][1000 genomes]
rs2633579	0.86[ASN][1000 genomes]
rs2633588	0.87[ASN][1000 genomes]
rs2633589	0.87[ASN][1000 genomes]
rs2638013	0.87[ASN][1000 genomes]
rs2638015	0.87[ASN][1000 genomes]
rs2638019	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2638023	0.87[ASN][1000 genomes]
rs2638026	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638027	0.81[AMR][1000 genomes]
rs2638028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638029	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638032	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2638035	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638039	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668215	0.89[AMR][1000 genomes]
rs2668219	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705505	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2705507	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2705515	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705518	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705519	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705521	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705522	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705525	0.87[ASN][1000 genomes]
rs2705541	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2705548	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2705552	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2705556	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705560	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705562	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2705565	0.86[ASN][1000 genomes]
rs2933134	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2933135	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933137	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2942061	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952319	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952320	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952324	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2952325	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2969895	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2969896	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2971204	0.86[ASN][1000 genomes]
rs3112268	0.86[ASN][1000 genomes]
rs728568	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751875	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766969	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998036	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112278200-112282000	Active TSS	K562	blood
2	chr3:112278200-112282200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:112278400-112282200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:112278600-112282400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:112278600-112283800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr3:112278800-112282000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr3:112278800-112282000	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr3:112278800-112282000	Active TSS	HSMM	muscle
9	chr3:112278800-112282200	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr3:112278800-112282200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:112278800-112282200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:112278800-112282200	Active TSS	Psoas Muscle	Psoas
13	chr3:112279000-112282000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:112279000-112282000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:112279000-112282000	Active TSS	Muscle Satellite Cultured Cells	--
16	chr3:112279000-112282000	Active TSS	Fetal Intestine Large	intestine
17	chr3:112279000-112282000	Active TSS	Fetal Intestine Small	intestine
18	chr3:112279000-112282000	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr3:112279000-112282000	Active TSS	GM12878-XiMat	blood
20	chr3:112279000-112282000	Active TSS	HMEC	breast
21	chr3:112279000-112282200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:112279000-112282200	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr3:112279000-112282200	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr3:112279000-112282200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:112279000-112282400	Active TSS	NHLF	lung
26	chr3:112279000-112282600	Active TSS	NHDF-Ad	bronchial
27	chr3:112279200-112282000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:112279200-112282000	Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr3:112279200-112282000	Active TSS	Monocytes-CD14+_RO01746	blood
30	chr3:112279200-112282200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:112279200-112282200	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr3:112279200-112282200	Active TSS	Placenta	Placenta
33	chr3:112279200-112282200	Active TSS	Right Ventricle	heart
34	chr3:112279400-112282000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:112279400-112282000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:112279400-112282000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:112279400-112282000	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr3:112279400-112282000	Active TSS	A549	lung
39	chr3:112279400-112282000	Active TSS	Hela-S3	cervix
40	chr3:112279400-112282000	Active TSS	NH-A	brain
41	chr3:112279400-112282200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:112279400-112282200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:112279400-112282200	Active TSS	Fetal Kidney	kidney
44	chr3:112279400-112282200	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr3:112279400-112282200	Active TSS	NHEK	skin
46	chr3:112279400-112283000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
47	chr3:112279600-112282000	Active TSS	H9 Cell Line	embryonic stem cell
48	chr3:112279600-112282000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:112279600-112282000	Active TSS	Aorta	Aorta
50	chr3:112279600-112282000	Active TSS	Brain Anterior Caudate	brain

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