Variant report

Variant	rs4683145
Chromosome Location	chr3:45864481-45864482
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45863759..45865356-chr3:45865550..45869231,3	K562	blood:
2	chr3:45862583..45864732-chr3:45872437..45875111,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12721497	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17078346	0.86[ASN][1000 genomes]
rs17078348	0.86[ASN][1000 genomes]
rs17078401	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2191032	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2673059	0.85[EUR][1000 genomes]
rs2742361	0.94[EUR][1000 genomes]
rs2742362	0.94[CEU][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs4683142	0.86[EUR][1000 genomes]
rs4683144	0.86[EUR][1000 genomes]
rs9843446	0.92[EUR][1000 genomes]
rs9843503	0.86[ASN][1000 genomes]
rs9856760	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv3796	chr3:45850961-45886045	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4683145	LIMD1	cis	parietal	SCAN
rs4683145	SLC6A20	cis	cerebellum	SCAN
rs4683145	SNRK	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45847800-45871400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:45849400-45864800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:45849400-45875200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:45849800-45871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:45850200-45866200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:45850200-45867800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:45850600-45868200	Weak transcription	Spleen	Spleen
8	chr3:45857800-45871600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:45858000-45882600	Weak transcription	A549	lung
10	chr3:45858400-45866000	Weak transcription	Fetal Brain Male	brain
11	chr3:45858400-45868400	Weak transcription	Fetal Kidney	kidney
12	chr3:45858400-45881200	Strong transcription	Dnd41	blood
13	chr3:45859400-45865000	Strong transcription	Brain Germinal Matrix	brain
14	chr3:45859400-45866000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:45859400-45868400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:45859600-45866000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:45859800-45871400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:45860000-45864800	Strong transcription	Fetal Stomach	stomach
19	chr3:45860000-45880000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:45860000-45882400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:45860200-45867600	Weak transcription	GM12878-XiMat	blood
22	chr3:45860400-45864800	Strong transcription	Thymus	Thymus
23	chr3:45860400-45867800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:45860400-45868000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:45860400-45868200	Strong transcription	Fetal Thymus	thymus
26	chr3:45860400-45868200	Weak transcription	Pancreas	Pancrea
27	chr3:45860400-45871600	Weak transcription	Esophagus	oesophagus
28	chr3:45860400-45871800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:45860400-45871800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:45860400-45875800	Weak transcription	Placenta	Placenta
31	chr3:45860400-45877400	Strong transcription	Liver	Liver
32	chr3:45860600-45865400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:45860600-45865800	Weak transcription	Osteobl	bone
34	chr3:45860600-45866000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:45860600-45874400	Weak transcription	HUVEC	blood vessel
36	chr3:45860800-45866000	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:45860800-45867200	Strong transcription	Primary T cells from cord blood	blood
38	chr3:45860800-45868400	Weak transcription	Gastric	stomach
39	chr3:45860800-45875200	Weak transcription	Aorta	Aorta
40	chr3:45861000-45882400	Weak transcription	Small Intestine	intestine
41	chr3:45861000-45882400	Weak transcription	NHDF-Ad	bronchial
42	chr3:45861000-45882600	Weak transcription	Stomach Mucosa	stomach
43	chr3:45861000-45882600	Weak transcription	Hela-S3	cervix
44	chr3:45861200-45866200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:45861200-45868200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:45861200-45879600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr3:45861200-45882400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:45861200-45882600	Weak transcription	Right Ventricle	heart
49	chr3:45861400-45867800	Weak transcription	NHEK	skin
50	chr3:45861400-45868200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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