Variant report

Variant	rs3200401
Chromosome Location	chr11:65271832-65271833
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10896004	0.81[ASN][1000 genomes]
rs10896005	0.83[ASN][1000 genomes]
rs10896006	0.83[ASN][1000 genomes]
rs10896008	0.83[ASN][1000 genomes]
rs10896009	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.83[ASN][1000 genomes]
rs10896010	0.83[ASN][1000 genomes]
rs10896012	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896015	0.83[JPT][hapmap];0.82[MEX][hapmap]
rs11227196	0.83[ASN][1000 genomes]
rs11227197	0.83[ASN][1000 genomes]
rs11227198	0.81[ASN][1000 genomes]
rs11227199	1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs11227201	0.83[ASN][1000 genomes]
rs11227202	0.83[ASN][1000 genomes]
rs11227205	0.84[ASN][1000 genomes]
rs11227206	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1194076	0.83[JPT][hapmap];0.82[MEX][hapmap]
rs12269965	0.83[ASN][1000 genomes]
rs12269975	0.83[ASN][1000 genomes]
rs12270054	0.83[JPT][hapmap];0.87[MEX][hapmap]
rs12294910	0.83[ASN][1000 genomes]
rs12360896	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.82[ASN][1000 genomes]
rs12364730	0.83[ASN][1000 genomes]
rs12788055	0.81[ASN][1000 genomes]
rs12808303	0.81[ASN][1000 genomes]
rs1346	0.84[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap]
rs17146964	1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.83[ASN][1000 genomes]
rs1783541	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap]
rs1787663	0.85[CEU][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap]
rs2508710	0.83[ASN][1000 genomes]
rs34527830	0.81[ASN][1000 genomes]
rs34582634	0.81[ASN][1000 genomes]
rs34877911	0.83[ASN][1000 genomes]
rs35292734	0.83[ASN][1000 genomes]
rs35469818	0.83[ASN][1000 genomes]
rs35826299	0.83[ASN][1000 genomes]
rs4102217	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7128776	0.83[ASN][1000 genomes]
rs7931615	0.82[ASN][1000 genomes]
rs947791	0.95[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897715	chr11:65083491-65427346	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
2	nsv897716	chr11:65083491-65481166	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	999 gene(s)	inside rSNPs	diseases
3	nsv541065	chr11:65117387-65271894	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	835 gene(s)	inside rSNPs	diseases
4	esv1829999	chr11:65136686-65343124	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	963 gene(s)	inside rSNPs	diseases
5	nsv897717	chr11:65140209-65278461	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	942 gene(s)	inside rSNPs	diseases
6	nsv897718	chr11:65140209-65577516	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1003 gene(s)	inside rSNPs	diseases
7	nsv541066	chr11:65142779-65271894	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	833 gene(s)	inside rSNPs	diseases
8	nsv541067	chr11:65142779-65313799	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	950 gene(s)	inside rSNPs	diseases
9	nsv541068	chr11:65142779-65331136	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	953 gene(s)	inside rSNPs	diseases
10	nsv541069	chr11:65142779-65368787	Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	965 gene(s)	inside rSNPs	diseases
11	nsv541070	chr11:65142779-65397058	Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	972 gene(s)	inside rSNPs	diseases
12	nsv541071	chr11:65142779-65429352	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	984 gene(s)	inside rSNPs	diseases
13	nsv897719	chr11:65157094-65335705	Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
14	nsv541072	chr11:65171202-65313799	Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	946 gene(s)	inside rSNPs	diseases
15	nsv541073	chr11:65171202-65331136	Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	949 gene(s)	inside rSNPs	diseases
16	nsv541074	chr11:65171202-65368787	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	961 gene(s)	inside rSNPs	diseases
17	nsv541075	chr11:65210592-65331136	Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	620 gene(s)	inside rSNPs	diseases
18	nsv541076	chr11:65210592-65397058	Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	645 gene(s)	inside rSNPs	diseases
19	nsv897720	chr11:65213434-65445950	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	665 gene(s)	inside rSNPs	diseases
20	nsv555210	chr11:65266169-65287251	Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	574 gene(s)	inside rSNPs	diseases
21	esv20791	chr11:65266587-65273530	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	516 gene(s)	inside rSNPs	diseases
22	nsv555211	chr11:65268469-65272325	Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	344 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3200401	ATG2A	cis	lymphoblastoid	seeQTL
rs3200401	LTBP3	cis	cerebellum	SCAN
rs3200401	SNX32	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65264600-65272800	Active TSS	Psoas Muscle	Psoas
2	chr11:65264800-65272200	Active TSS	Fetal Intestine Small	intestine
3	chr11:65265400-65272000	ZNF genes & repeats	Fetal Brain Male	brain
4	chr11:65266800-65272400	ZNF genes & repeats	Fetal Heart	heart
5	chr11:65266800-65274000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
6	chr11:65266800-65274200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:65267000-65273600	Transcr. at gene 5' and 3'	Fetal Lung	lung
8	chr11:65267000-65273800	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr11:65267000-65273800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
10	chr11:65267000-65274200	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
11	chr11:65267200-65273600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:65267200-65273800	Transcr. at gene 5' and 3'	K562	blood
13	chr11:65267200-65274000	Transcr. at gene 5' and 3'	Dnd41	blood
14	chr11:65267200-65274200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:65267400-65273800	Transcr. at gene 5' and 3'	NHEK	skin
16	chr11:65267400-65273800	Transcr. at gene 5' and 3'	Osteobl	bone
17	chr11:65267400-65274000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr11:65267400-65274200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:65267400-65274200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
20	chr11:65267400-65274400	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
21	chr11:65267600-65272200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood
22	chr11:65267600-65273400	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
23	chr11:65267600-65273600	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
24	chr11:65267600-65273800	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
25	chr11:65267600-65273800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:65267600-65273800	Transcr. at gene 5' and 3'	HMEC	breast
27	chr11:65267600-65274000	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
28	chr11:65267600-65274000	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
29	chr11:65267600-65274200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
30	chr11:65267600-65274200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
31	chr11:65267600-65274400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:65267600-65274400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
33	chr11:65267800-65272800	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:65267800-65273200	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
35	chr11:65267800-65273400	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
36	chr11:65267800-65273400	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
37	chr11:65267800-65273400	Transcr. at gene 5' and 3'	NHLF	lung
38	chr11:65267800-65273600	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
39	chr11:65267800-65273600	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
40	chr11:65267800-65273800	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
41	chr11:65267800-65273800	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
42	chr11:65267800-65273800	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
43	chr11:65267800-65274000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
44	chr11:65267800-65274000	Transcr. at gene 5' and 3'	HSMM	muscle
45	chr11:65267800-65274200	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
46	chr11:65267800-65274200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
47	chr11:65267800-65274200	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
48	chr11:65267800-65274200	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
49	chr11:65267800-65274200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
50	chr11:65267800-65274400	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood

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