Variant report

Variant	rs2227929
Chromosome Location	chr3:142277536-142277537
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10935463	0.81[EUR][1000 genomes]
rs1129391	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11708470	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11715514	0.82[EUR][1000 genomes]
rs11718899	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11916455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11923612	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11928203	0.85[ASW][hapmap]
rs12629001	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12629713	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12634255	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12638158	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12639363	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13063075	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13065800	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13066441	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13068397	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13070239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13071750	0.85[CEU][hapmap]
rs13072346	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13072355	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13075259	0.81[EUR][1000 genomes]
rs13082648	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap]
rs13085247	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13085261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13089219	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13092234	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13092593	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13093304	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13099184	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2140437	0.85[ASW][hapmap]
rs2227931	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2306699	0.91[CHB][hapmap]
rs34392719	0.85[CEU][hapmap];0.92[GIH][hapmap];0.89[TSI][hapmap]
rs3923464	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4256152	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4558780	0.83[EUR][1000 genomes]
rs4582075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4683427	0.81[TSI][hapmap]
rs57299906	0.83[ASN][1000 genomes]
rs6440085	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6776402	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786320	0.89[CHB][hapmap]
rs6809448	0.85[ASW][hapmap];0.87[GIH][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap]
rs7432464	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7623785	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap]
rs7636909	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7641914	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7643377	0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap]
rs953135	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap]
rs9814159	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap]
rs9829125	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap]
rs9859834	0.91[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap]
rs9867210	0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap]

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	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv933680	chr3:142211643-142287189	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv591919	chr3:142219542-142308070	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2227929	XRN1	cis	cerebellum	SCAN
rs2227929	TRPC1	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142204200-142281400	Weak transcription	Colonic Mucosa	Colon
2	chr3:142226000-142287200	Weak transcription	Right Ventricle	heart
3	chr3:142231600-142295800	Weak transcription	Small Intestine	intestine
4	chr3:142240800-142281600	Weak transcription	Fetal Brain Male	brain
5	chr3:142241000-142280800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:142244400-142295600	Weak transcription	Fetal Heart	heart
7	chr3:142248400-142287400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:142253400-142284800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:142253400-142284800	Weak transcription	Brain Substantia Nigra	brain
10	chr3:142253800-142296400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:142256200-142283600	Weak transcription	Aorta	Aorta
12	chr3:142259800-142285600	Strong transcription	Dnd41	blood
13	chr3:142263000-142285400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:142263400-142286200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr3:142263600-142288000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:142263800-142285600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:142263800-142286600	Strong transcription	Liver	Liver
18	chr3:142264000-142279200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:142264000-142285200	Strong transcription	Fetal Thymus	thymus
20	chr3:142265200-142285000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr3:142265200-142287600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:142265400-142283600	Weak transcription	HSMMtube	muscle
23	chr3:142266200-142278600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:142266400-142285600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:142267000-142286600	Strong transcription	Primary B cells from cord blood	blood
26	chr3:142267400-142279200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:142267600-142282000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:142267800-142279200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr3:142267800-142285200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr3:142268800-142284200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:142269200-142278000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:142269200-142292600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:142269400-142277800	Weak transcription	NHDF-Ad	bronchial
34	chr3:142270000-142287200	Weak transcription	Pancreas	Pancrea
35	chr3:142270200-142285000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:142270800-142285200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:142270800-142286400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:142271000-142279000	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:142271000-142285400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:142271800-142282200	Weak transcription	Fetal Kidney	kidney
41	chr3:142271800-142285200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:142272200-142286200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:142272400-142282200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:142272600-142279800	Weak transcription	Fetal Lung	lung
45	chr3:142272600-142280200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:142272600-142282000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:142272600-142283600	Weak transcription	Fetal Brain Female	brain
48	chr3:142272600-142284800	Weak transcription	HepG2	liver
49	chr3:142272600-142287400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:142272600-142296200	Weak transcription	Brain Angular Gyrus	brain

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