Variant report

Variant	rs329499
Chromosome Location	chr2:64324076-64324077
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2581047	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs329500	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6726519	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6746080	0.82[EUR][1000 genomes]
rs7562080	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7581647	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7604693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34698	chr2:64312142-64521366	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv34955	chr2:64312182-64521290	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv834243	chr2:64316514-64476935	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs329499	PELI1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64313200-64341800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:64314400-64325000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:64316600-64324800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:64316800-64326200	Strong transcription	Primary T cells from cord blood	blood
5	chr2:64316800-64327400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:64316800-64327800	Strong transcription	Fetal Thymus	thymus
7	chr2:64317000-64328000	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr2:64317200-64335600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr2:64317600-64327000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:64317800-64333200	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr2:64318200-64324600	Strong transcription	Fetal Intestine Large	intestine
12	chr2:64318200-64333600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:64318400-64327000	Strong transcription	Liver	Liver
14	chr2:64318400-64327400	Strong transcription	Placenta	Placenta
15	chr2:64318400-64327600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:64318400-64327800	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr2:64318400-64327800	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr2:64318400-64328000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:64318400-64335600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:64318800-64327000	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr2:64318800-64336400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:64319600-64327600	Strong transcription	HUVEC	blood vessel
23	chr2:64319800-64327000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr2:64320200-64328000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:64320400-64324200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:64320400-64326200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:64320400-64339200	Weak transcription	NHLF	lung
28	chr2:64320600-64324400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:64320600-64324400	Strong transcription	Adipose Nuclei	Adipose
30	chr2:64320600-64324400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr2:64320600-64324400	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:64320600-64326200	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr2:64320600-64327400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr2:64320600-64332200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:64320800-64327800	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:64321000-64324400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:64321000-64327400	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr2:64321000-64332200	Weak transcription	Hela-S3	cervix
39	chr2:64321200-64324400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr2:64321200-64324600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:64321200-64330400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:64321400-64324200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:64321600-64327000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr2:64321600-64327800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:64321800-64324200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:64321800-64324200	Strong transcription	Fetal Brain Female	brain
47	chr2:64321800-64324400	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr2:64321800-64324400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:64321800-64324400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr2:64321800-64324400	Strong transcription	Colon Smooth Muscle	Colon

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