Variant report

Variant	rs3817657
Chromosome Location	chr11:4142592-4142593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10742242	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10767811	0.81[CHB][hapmap]
rs10767845	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10835508	0.81[CHB][hapmap]
rs10835521	0.81[CHB][hapmap]
rs10835540	0.81[CHB][hapmap]
rs10835556	0.81[CHB][hapmap]
rs10835561	0.81[CHB][hapmap]
rs10835596	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs10835604	0.81[CHB][hapmap]
rs10835611	0.95[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10835684	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10835719	0.84[TSI][hapmap]
rs11030639	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs11030781	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs11030918	0.87[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs11031110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12290828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12806698	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs1442726	0.81[CHB][hapmap]
rs2044135	0.84[TSI][hapmap]
rs2056853	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165728	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2268168	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284450	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34832073	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35359151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910599	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4910877	0.81[CHB][hapmap]
rs4910886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910887	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4910888	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4910889	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4910904	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7111104	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7130580	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7932702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7940013	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7949663	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs963998	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs9666229	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9666857	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv832053	chr11:4096527-4330263	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1053189	chr11:4123119-4359044	Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1048590	chr11:4133055-4225100	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv540911	chr11:4133055-4225100	Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1053482	chr11:4138062-4276133	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3817657	TRIM5	cis	cerebellum	SCAN
rs3817657	ANO9	cis	parietal	SCAN
rs3817657	RRM1	cis	Artery Tibial	GTEx
rs3817657	TRIM21	cis	cerebellum	SCAN
rs3817657	RRM1	cis	cerebellum	SCAN
rs3817657	IFITM5	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4117600-4144600	Weak transcription	HSMMtube	muscle
2	chr11:4117600-4145200	Weak transcription	Gastric	stomach
3	chr11:4117600-4153000	Weak transcription	Stomach Mucosa	stomach
4	chr11:4117800-4147800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:4117800-4160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr11:4118000-4159200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:4118400-4146400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr11:4118400-4156200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:4119400-4157600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr11:4121000-4159400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr11:4121600-4142800	Weak transcription	Fetal Brain Male	brain
12	chr11:4122400-4158000	Strong transcription	Dnd41	blood
13	chr11:4122800-4158000	Strong transcription	Fetal Thymus	thymus
14	chr11:4123000-4152000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:4123000-4157600	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr11:4123000-4157600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr11:4123000-4157800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:4123200-4158000	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr11:4124000-4157600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr11:4124000-4157800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:4126600-4166600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr11:4127000-4151000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:4127400-4148400	Weak transcription	Psoas Muscle	Psoas
24	chr11:4127600-4144400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr11:4127600-4144400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr11:4127600-4158000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr11:4130200-4144600	Weak transcription	Fetal Heart	heart
28	chr11:4131000-4150400	Strong transcription	Primary T cells from cord blood	blood
29	chr11:4131000-4157400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr11:4132200-4151600	Strong transcription	Primary hematopoietic stem cells	blood
31	chr11:4134200-4144400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr11:4135000-4143000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr11:4137200-4149800	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr11:4137400-4156600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr11:4137600-4143000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr11:4137600-4150600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr11:4137800-4144400	Weak transcription	Spleen	Spleen
38	chr11:4137800-4144600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:4137800-4158000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr11:4138000-4148200	Weak transcription	Pancreas	Pancrea
41	chr11:4138000-4149200	Strong transcription	Liver	Liver
42	chr11:4138200-4144400	Weak transcription	Right Ventricle	heart
43	chr11:4138200-4160600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:4138400-4143600	Strong transcription	GM12878-XiMat	blood
45	chr11:4138400-4155600	Strong transcription	Hela-S3	cervix
46	chr11:4138600-4157600	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr11:4138600-4158000	Strong transcription	Primary B cells from peripheral blood	blood
48	chr11:4138800-4157400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr11:4138800-4158000	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr11:4138800-4160400	Strong transcription	Placenta	Placenta

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