Variant report

Variant	rs4332959
Chromosome Location	chr2:96549121-96549122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11164053	0.89[EUR][1000 genomes]
rs11683523	0.89[EUR][1000 genomes]
rs11689832	0.88[EUR][1000 genomes]
rs11691090	0.80[EUR][1000 genomes]
rs11695514	0.90[EUR][1000 genomes]
rs12464148	0.84[ASN][1000 genomes]
rs12477206	0.85[EUR][1000 genomes]
rs28856333	0.86[ASN][1000 genomes]
rs34233881	0.84[ASN][1000 genomes]
rs4062989	0.80[EUR][1000 genomes]
rs4527246	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4907217	0.85[EUR][1000 genomes]
rs4907219	0.81[EUR][1000 genomes]
rs4907224	0.82[EUR][1000 genomes]
rs56791141	0.84[ASN][1000 genomes]
rs60273147	0.88[EUR][1000 genomes]
rs61409777	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62153670	0.85[EUR][1000 genomes]
rs62153678	0.89[EUR][1000 genomes]
rs62153679	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62153692	0.88[EUR][1000 genomes]
rs62153700	0.82[EUR][1000 genomes]
rs62156932	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3416818	chr2:96072529-96680708	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv874660	chr2:96091132-96669134	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv516044	chr2:96150959-96683378	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1003371	chr2:96326106-96684876	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv874662	chr2:96334397-96578621	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv874665	chr2:96370571-96596515	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv874666	chr2:96370571-96691125	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1004482	chr2:96408987-96596717	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Bivalent Enhancer	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv834303	chr2:96432935-96551704	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv428054	chr2:96438238-96627125	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv961832	chr2:96453677-96671971	Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv874667	chr2:96465201-96596515	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv874668	chr2:96465201-96600569	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
14	esv1826589	chr2:96468292-96583910	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
15	esv1826305	chr2:96468492-96583710	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
16	esv1848259	chr2:96477989-96583252	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv834304	chr2:96493545-96667472	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv10093	chr2:96524159-96583335	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
19	esv1847850	chr2:96532929-96582175	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
20	nsv508154	chr2:96534336-96609925	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
21	esv1849015	chr2:96534572-96581975	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv1004486	chr2:96544604-96684876	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
23	esv1847704	chr2:96545150-96583452	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
24	esv3506800	chr2:96545563-96588565	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
25	esv3506801	chr2:96545563-96588565	Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases
26	nsv874669	chr2:96547820-96691125	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4332959	GPAT2	cis	Adipose Subcutaneous	GTEx
rs4332959	FAHD2CP	cis	Muscle Skeletal	GTEx
rs4332959	GPAT2	cis	Muscle Skeletal	GTEx
rs4332959	AC008268.2	cis	Adipose Subcutaneous	GTEx
rs4332959	ADRA2B	cis	Thyroid	GTEx
rs4332959	FAHD2CP	cis	Adipose Subcutaneous	GTEx
rs4332959	FAHD2CP	cis	lung	GTEx
rs4332959	ADRA2B	cis	Nerve Tibial	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96500600-96553400	Weak transcription	Brain Anterior Caudate	brain
2	chr2:96502600-96561400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:96502800-96551400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:96502800-96555200	Weak transcription	Ovary	ovary
5	chr2:96502800-96585000	Weak transcription	Left Ventricle	heart
6	chr2:96502800-96616600	Weak transcription	Fetal Stomach	stomach
7	chr2:96503000-96563600	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:96506200-96549400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:96506600-96562000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:96516200-96549200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:96516800-96553400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:96521800-96555600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:96526600-96549400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:96526600-96555200	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:96526800-96553000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:96526800-96555200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:96526800-96557600	Weak transcription	NHDF-Ad	bronchial
18	chr2:96527800-96554000	Weak transcription	HUVEC	blood vessel
19	chr2:96528600-96555600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:96528600-96560000	Weak transcription	Fetal Intestine Large	intestine
21	chr2:96530600-96555200	Weak transcription	Fetal Brain Female	brain
22	chr2:96531200-96557800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr2:96533000-96558000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:96536000-96576800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:96539000-96549200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:96541000-96555200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:96541000-96555800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:96541000-96582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:96541000-96595400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:96541200-96559800	Weak transcription	HMEC	breast
31	chr2:96541600-96595200	Weak transcription	Fetal Brain Male	brain
32	chr2:96542400-96557200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:96542600-96558400	Weak transcription	Brain Substantia Nigra	brain
34	chr2:96543000-96555200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr2:96543400-96549200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:96543800-96596200	Weak transcription	K562	blood
37	chr2:96544000-96555800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:96544600-96561800	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:96544800-96557200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr2:96545000-96549200	Weak transcription	Primary T cells from cord blood	blood
41	chr2:96545000-96559600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr2:96545000-96576400	Weak transcription	Brain Germinal Matrix	brain
43	chr2:96546000-96555600	Weak transcription	Fetal Lung	lung
44	chr2:96546000-96577400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:96546400-96559800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:96546600-96549200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr2:96546600-96554000	Weak transcription	HSMM	muscle
48	chr2:96546800-96549200	Weak transcription	Liver	Liver
49	chr2:96546800-96549200	Weak transcription	Fetal Muscle Trunk	muscle
50	chr2:96546800-96562200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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