Variant report

Variant	rs1868180
Chromosome Location	chr3:143506341-143506342
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11706302	0.81[CEU][hapmap]
rs11720499	0.83[CEU][hapmap]
rs12233446	0.83[CEU][hapmap]
rs16854291	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16854322	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16854336	0.88[CEU][hapmap]
rs2121771	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2121775	0.82[CEU][hapmap]
rs57830957	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6800578	0.83[CEU][hapmap]
rs6807571	0.81[CEU][hapmap]

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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers 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
2	esv3418674	chr3:143457005-143558357	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1009935	chr3:143497700-143610852	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1868180	TFDP2	cis	parietal	SCAN
rs1868180	NRG3	trans	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143492400-143513000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:143494800-143515600	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr3:143494800-143515800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:143499600-143512800	Weak transcription	Primary T cells from cord blood	blood
5	chr3:143505600-143508000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:143505800-143510200	Weak transcription	Primary B cells from cord blood	blood
7	chr3:143505800-143510800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:143505800-143513800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr3:143505800-143514800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:143505800-143514800	Weak transcription	Lung	lung
11	chr3:143505800-143515400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:143505800-143525800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:143506000-143506400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:143506000-143506400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:143506000-143506400	Enhancers	Brain Angular Gyrus	brain
16	chr3:143506000-143506400	Enhancers	Brain Cingulate Gyrus	brain
17	chr3:143506000-143506400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr3:143506000-143506400	Enhancers	Brain Substantia Nigra	brain
19	chr3:143506000-143506400	Enhancers	Colon Smooth Muscle	Colon
20	chr3:143506000-143506400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr3:143506000-143506400	Enhancers	Rectal Smooth Muscle	rectum
22	chr3:143506000-143506600	Enhancers	Brain Anterior Caudate	brain
23	chr3:143506000-143506600	Enhancers	Fetal Lung	lung
24	chr3:143506000-143510200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:143506000-143512600	Weak transcription	Adipose Nuclei	Adipose
26	chr3:143506000-143512800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:143506000-143513200	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:143506000-143514800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:143506000-143521200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr3:143506200-143506400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:143506200-143506400	Enhancers	Brain Hippocampus Middle	brain
32	chr3:143506200-143506600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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