Variant report

Variant	rs1868179
Chromosome Location	chr3:143505568-143505569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11706563	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12488854	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491888	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059339	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13061222	0.80[EUR][1000 genomes]
rs13066023	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13073355	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13091085	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2166773	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166774	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2361198	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs36086202	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4839609	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56300534	0.80[EUR][1000 genomes]
rs6805483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs746351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1868179	NRG3	trans	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

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	chr3:143503200-143505600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:143503200-143505600	Weak transcription	HSMMtube	muscle
7	chr3:143504000-143505600	Weak transcription	HSMM	muscle
8	chr3:143505200-143505600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:143505200-143505600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:143505200-143505600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:143505200-143505600	Enhancers	Brain Anterior Caudate	brain
12	chr3:143505200-143505600	Flanking Active TSS	Brain Hippocampus Middle	brain
13	chr3:143505200-143505600	Enhancers	Brain Substantia Nigra	brain
14	chr3:143505200-143505600	Enhancers	Fetal Muscle Leg	muscle
15	chr3:143505200-143505600	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr3:143505200-143505600	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr3:143505200-143505800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:143505200-143505800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:143505200-143505800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr3:143505200-143505800	Enhancers	Primary B cells from cord blood	blood
21	chr3:143505200-143505800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr3:143505200-143505800	Enhancers	Placenta	Placenta
23	chr3:143505200-143505800	Flanking Active TSS	Ovary	ovary
24	chr3:143505200-143505800	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr3:143505200-143505800	Enhancers	NHDF-Ad	bronchial
26	chr3:143505200-143505800	Enhancers	NHLF	lung
27	chr3:143505200-143506000	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:143505200-143506000	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr3:143505200-143506000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:143505200-143506000	Enhancers	Primary B cells from peripheral blood	blood
31	chr3:143505200-143506000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:143505200-143506000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:143505200-143506000	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr3:143505200-143506000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:143505200-143506000	Enhancers	Fetal Stomach	stomach
36	chr3:143505200-143506200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:143505200-143506200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:143505200-143506200	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr3:143505200-143506200	Enhancers	Fetal Heart	heart
40	chr3:143505400-143505600	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr3:143505400-143505600	Active TSS	Aorta	Aorta
42	chr3:143505400-143505600	Enhancers	NHEK	skin
43	chr3:143505400-143505600	Enhancers	Osteobl	bone
44	chr3:143505400-143505800	Enhancers	H1 Cell Line	embryonic stem cell
45	chr3:143505400-143505800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:143505400-143505800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:143505400-143505800	Flanking Active TSS	Right Atrium	heart
48	chr3:143505400-143505800	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr3:143505400-143506000	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr3:143505400-143506000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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