Variant report

Variant	rs57916312
Chromosome Location	chr3:160940074-160940075
allele	C/T
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:8)
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	MXI1	chr3:160938485-160940211	IMR90	lung:	n/a	n/a
2	ZNF384	chr3:160939510-160940315	GM12878	blood:	n/a	n/a
3	CHD1	chr3:160939526-160940080	H1-hESC	embryonic stem cell:	n/a	n/a
4	HCFC1	chr3:160938368-160940220	Hela-S3	cervix:	n/a	n/a
5	SIN3AK20	chr3:160938568-160940225	MCF-7	breast:	n/a	n/a
6	POLR2A	chr3:160938290-160940780	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr3:160938583-160940388	MCF-7	breast:	n/a	n/a
8	MAZ	chr3:160938678-160940153	IMR90	lung:	n/a	n/a
9	SIN3AK20	chr3:160938504-160940237	MCF-7	breast:	n/a	n/a
10	MAX	chr3:160938482-160940096	MCF-7	breast:	n/a	n/a
11	POLR2A	chr3:160938251-160940135	IMR90	lung:	n/a	n/a
12	CHD1	chr3:160938248-160941179	IMR90	lung:	n/a	n/a
13	POLR2A	chr3:160938253-160940262	Hela-S3	cervix:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160937993..160941056-chr3:161047965..161051023,3	MCF-7	breast:
2	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
3	chr3:160938091..160940577-chr7:104653089..104654973,2	MCF-7	breast:
4	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
5	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
6	chr3:160816932..160819441-chr3:160937058..160940131,3	MCF-7	breast:
7	chr3:160821182..160827138-chr3:160937374..160941314,7	MCF-7	breast:
8	chr3:160940058..160942666-chr3:161042036..161044035,3	MCF-7	breast:

No data

Variant related genes	Relation type
NMD3	TF binding region
ENSG00000243838	Chromatin interaction
ENSG00000240138	Chromatin interaction
ENSG00000169255	Chromatin interaction
ENSG00000005483	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000239569	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12634006	0.86[EUR][1000 genomes]
rs17392097	0.87[ASN][1000 genomes]
rs28713364	0.95[EUR][1000 genomes]
rs34759927	1.00[AMR][1000 genomes]
rs35590548	1.00[AMR][1000 genomes]
rs36015194	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57278490	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57496534	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57655051	1.00[ASN][1000 genomes]
rs57803909	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57974280	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58350275	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58562874	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58739937	1.00[ASN][1000 genomes]
rs58878734	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59371901	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59761692	0.86[EUR][1000 genomes]
rs59964190	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60612225	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60684226	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60866328	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61217744	0.86[EUR][1000 genomes]
rs62282277	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441363	0.86[EUR][1000 genomes]
rs6788738	0.95[EUR][1000 genomes]
rs6798468	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73023224	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73878307	0.86[EUR][1000 genomes]
rs73878308	0.86[EUR][1000 genomes]
rs73878311	0.86[EUR][1000 genomes]
rs7625217	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs873183	0.86[EUR][1000 genomes]
rs896080	0.86[EUR][1000 genomes]
rs9834806	0.95[EUR][1000 genomes]
rs9839335	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers 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 target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160938000-160940400	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr3:160938200-160940400	Active TSS	A549	lung
3	chr3:160938200-160940600	Active TSS	Brain Cingulate Gyrus	brain
4	chr3:160938200-160940600	Active TSS	Brain Hippocampus Middle	brain
5	chr3:160938200-160940600	Active TSS	Right Atrium	heart
6	chr3:160938200-160940600	Active TSS	Thymus	Thymus
7	chr3:160938200-160940600	Active TSS	HSMM	muscle
8	chr3:160938400-160940400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:160938400-160940400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr3:160938400-160940400	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr3:160938400-160940600	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr3:160938400-160940600	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr3:160938400-160940600	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr3:160938400-160940600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:160938400-160940600	Active TSS	GM12878-XiMat	blood
16	chr3:160938400-160940600	Active TSS	NH-A	brain
17	chr3:160938400-160940800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:160938400-160941200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:160938400-160941400	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr3:160938400-160941600	Active TSS	Stomach Smooth Muscle	stomach
21	chr3:160938600-160940200	Active TSS	Placenta	Placenta
22	chr3:160938600-160940400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:160938600-160940400	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr3:160938600-160940400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:160938600-160940400	Active TSS	Brain Angular Gyrus	brain
26	chr3:160938600-160940600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:160938600-160940600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:160938600-160940600	Active TSS	Brain Anterior Caudate	brain
29	chr3:160938600-160940600	Active TSS	Fetal Intestine Large	intestine
30	chr3:160938600-160940600	Active TSS	Fetal Thymus	thymus
31	chr3:160938600-160940600	Active TSS	Left Ventricle	heart
32	chr3:160938600-160940600	Active TSS	Ovary	ovary
33	chr3:160938600-160940600	Active TSS	Psoas Muscle	Psoas
34	chr3:160938600-160940600	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr3:160938600-160940800	Active TSS	H9 Cell Line	embryonic stem cell
36	chr3:160938600-160940800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:160938600-160940800	Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr3:160938600-160940800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:160938600-160940800	Active TSS	Colonic Mucosa	Colon
40	chr3:160938600-160940800	Active TSS	Fetal Muscle Trunk	muscle
41	chr3:160938600-160940800	Active TSS	HSMMtube	muscle
42	chr3:160938600-160941000	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr3:160938600-160941000	Active TSS	Lung	lung
44	chr3:160938600-160941400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:160938600-160941400	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr3:160938600-160941600	Active TSS	H1 Cell Line	embryonic stem cell
47	chr3:160938600-160941600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:160938600-160941600	Active TSS	NHLF	lung
49	chr3:160938600-160942400	Active TSS	Right Ventricle	heart
50	chr3:160938800-160940200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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