Variant report

Variant	rs57630131
Chromosome Location	chr3:52277445-52277446
allele	A/G
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	chr3:52277359-52278451	K562	blood:	n/a	n/a
2	SETDB1	chr3:52277232-52278048	U2OS	brain:	n/a	n/a
3	MTA3	chr3:52277397-52279759	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52277093..52279461-chr3:52290667..52292256,2	MCF-7	breast:
2	chr3:52027463..52030131-chr3:52273399..52277503,3	K562	blood:

Variant related genes	Relation type
TWF2	TF binding region
PPM1M	TF binding region
TLR9	TF binding region
ENSG00000162244	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1060330	0.82[ASN][1000 genomes]
rs11717383	0.83[ASN][1000 genomes]
rs1546737	0.85[EUR][1000 genomes]
rs2267847	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2276834	0.80[ASN][1000 genomes]
rs34228726	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34569561	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs353547	0.84[ASN][1000 genomes]
rs3844291	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3852063	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3852064	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57615517	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59565798	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6445358	0.82[ASN][1000 genomes]
rs7614727	0.82[ASN][1000 genomes]
rs7618915	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7622851	0.81[ASN][1000 genomes]
rs7629072	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
8	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
9	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
10	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
11	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS 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 miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
12	nsv876790	chr3:52261382-52286825	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv876791	chr3:52269491-52286825	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57630131	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52274400-52278800	Weak transcription	Fetal Lung	lung
2	chr3:52274400-52279000	Weak transcription	Fetal Heart	heart
3	chr3:52274400-52279400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:52274600-52277600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:52274600-52277600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:52274600-52278000	Weak transcription	Esophagus	oesophagus
7	chr3:52274600-52278200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:52274600-52278400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr3:52274600-52279000	Weak transcription	Brain Anterior Caudate	brain
10	chr3:52274600-52279000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:52274800-52277800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:52274800-52278000	Weak transcription	Left Ventricle	heart
13	chr3:52274800-52278200	Weak transcription	Colonic Mucosa	Colon
14	chr3:52274800-52278600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:52274800-52278800	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:52274800-52279200	Weak transcription	Liver	Liver
17	chr3:52274800-52279200	Weak transcription	Pancreas	Pancrea
18	chr3:52274800-52279200	Weak transcription	Right Atrium	heart
19	chr3:52275000-52277600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:52275000-52277600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:52275000-52277600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:52275000-52277600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:52275000-52277600	Weak transcription	Placenta	Placenta
24	chr3:52275000-52277600	Weak transcription	Lung	lung
25	chr3:52275000-52277600	Weak transcription	Spleen	Spleen
26	chr3:52275000-52277600	Weak transcription	HUVEC	blood vessel
27	chr3:52275000-52277800	Weak transcription	NH-A	brain
28	chr3:52275000-52278000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:52275000-52278000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:52275000-52278000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:52275000-52278000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr3:52275000-52278000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:52275000-52278000	Weak transcription	Right Ventricle	heart
34	chr3:52275000-52278000	Weak transcription	HSMMtube	muscle
35	chr3:52275000-52278800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:52275000-52279000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:52275000-52279200	Weak transcription	Stomach Mucosa	stomach
38	chr3:52275200-52277600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:52275200-52277600	Weak transcription	Hela-S3	cervix
40	chr3:52275200-52277600	Weak transcription	HMEC	breast
41	chr3:52275200-52277800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:52275200-52277800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:52275200-52277800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:52275200-52277800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr3:52275200-52277800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:52275200-52277800	Weak transcription	NHEK	skin
47	chr3:52275200-52278000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:52275200-52278000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:52275200-52278000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:52275200-52278000	Weak transcription	NHDF-Ad	bronchial

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