Variant report

Variant	rs9821843
Chromosome Location	chr3:139654466-139654467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10935361	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11707263	0.96[ASN][1000 genomes]
rs12495959	0.87[ASN][1000 genomes]
rs13063473	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13075026	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13085522	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1834504	0.89[ASN][1000 genomes]
rs1895858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2059572	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28413505	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35556479	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56370145	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6439885	0.88[ASN][1000 genomes]
rs67605525	0.96[ASN][1000 genomes]
rs733774	0.81[EUR][1000 genomes]
rs959555	0.86[ASN][1000 genomes]
rs976108	0.82[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9815926	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9821708	0.81[EUR][1000 genomes]
rs983323	0.89[ASN][1000 genomes]
rs9850110	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9850149	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9869519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9878008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv998423	chr3:139526446-139947336	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv877544	chr3:139642572-139688415	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3486576	chr3:139652862-139656260	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3486577	chr3:139652862-139656260	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9821843	TRPC1	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139653200-139654800	Active TSS	Brain Anterior Caudate	brain
2	chr3:139653200-139655000	Active TSS	Brain Cingulate Gyrus	brain
3	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
5	chr3:139653200-139655200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr3:139653200-139655400	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr3:139653200-139655600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
8	chr3:139653200-139655600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr3:139653200-139656000	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr3:139653400-139654600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:139653400-139654600	Active TSS	Fetal Brain Female	brain
12	chr3:139653400-139654600	Active TSS	Fetal Kidney	kidney
13	chr3:139653400-139654800	Active TSS	Brain Substantia Nigra	brain
14	chr3:139653400-139655000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
15	chr3:139653400-139655000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:139653400-139655000	Flanking Active TSS	Pancreas	Pancrea
17	chr3:139653400-139655000	Bivalent/Poised TSS	A549	lung
18	chr3:139653400-139655200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:139653400-139655200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:139653400-139655200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr3:139653400-139655400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
22	chr3:139653400-139655400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:139653400-139655600	Bivalent Enhancer	Liver	Liver
24	chr3:139653400-139656200	Active TSS	Brain Angular Gyrus	brain
25	chr3:139653400-139657000	Active TSS	HSMMtube	muscle
26	chr3:139653600-139654600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:139653600-139654600	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
28	chr3:139653600-139654600	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
29	chr3:139653600-139654800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr3:139653600-139655000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:139653600-139655000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:139653600-139655400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
33	chr3:139653600-139655600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:139653600-139655600	Active TSS	Right Atrium	heart
35	chr3:139653600-139656600	Active TSS	Ovary	ovary
36	chr3:139653800-139654600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
37	chr3:139653800-139654600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
38	chr3:139653800-139654800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
39	chr3:139653800-139655200	Enhancers	Fetal Heart	heart
40	chr3:139653800-139655200	Bivalent/Poised TSS	Thymus	Thymus
41	chr3:139653800-139655400	Bivalent/Poised TSS	Psoas Muscle	Psoas
42	chr3:139654000-139654800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
43	chr3:139654000-139654800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
44	chr3:139654000-139654800	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
45	chr3:139654000-139655000	Bivalent/Poised TSS	NHLF	lung
46	chr3:139654000-139655200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
47	chr3:139654000-139655400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:139654200-139654600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:139654200-139654600	Flanking Bivalent TSS/Enh	Lung	lung
50	chr3:139654200-139654600	Flanking Bivalent TSS/Enh	Placenta Amnion	Placenta Amnion

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