Variant report

Variant	rs11901025
Chromosome Location	chr2:87278601-87278602
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10205992	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55984711	0.83[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	nsv532319	chr2:87024867-88005418	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv1800069	chr2:87056027-87885905	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1010107	chr2:87105444-88052318	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
4	nsv519198	chr2:87108211-87771196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
5	esv33176	chr2:87122115-87325330	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1803562	chr2:87126250-88038663	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
7	nsv997663	chr2:87126250-88052318	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
8	esv2757815	chr2:87155912-88042080	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
9	esv1796172	chr2:87245762-88042080	Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
10	nsv428398	chr2:87245762-88042080	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
11	esv1801752	chr2:87245762-88123177	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
12	nsv1002590	chr2:87250484-87960588	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
13	nsv1011527	chr2:87250484-88052318	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
14	nsv10065	chr2:87255641-87345941	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	esv16360	chr2:87257509-87280275	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
16	esv1801854	chr2:87258404-87284657	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	esv1799620	chr2:87258404-87287209	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	esv1792532	chr2:87258604-87279929	Weak transcription Enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases
19	esv1798887	chr2:87258604-87283090	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	esv1795827	chr2:87258604-87294659	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
21	nsv1000885	chr2:87260341-87849159	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
22	nsv1003162	chr2:87260341-87960588	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
23	nsv1014950	chr2:87260341-88024655	Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
24	nsv874476	chr2:87262856-87424779	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
25	nsv874477	chr2:87262856-87453247	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
26	nsv963634	chr2:87276522-87279295	Weak transcription Strong transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs11901025	PLGLA1///PLGLB1///PLGLB2	N/A	lymphoblastoid	RTeQTL
rs11901025	PLGLB2	cis	Adipose Subcutaneous	GTEx
rs11901025	AC125232.1	cis	Heart Left Ventricle	GTEx
rs11901025	AC125232.1	cis	Muscle Skeletal	GTEx
rs11901025	AC125232.1	cis	Artery Tibial	GTEx
rs11901025	AC125232.1	cis	Esophagus Mucosa	GTEx
rs11901025	AC125232.1	cis	Adipose Subcutaneous	GTEx
rs11901025	AC125232.1	cis	lung	GTEx
rs11901025	AC125232.1	cis	Thyroid	GTEx
rs11901025	LOC285074	Cis_1M	lymphoblastoid	RTeQTL
rs11901025	AC125232.1	cis	Stomach	GTEx
rs11901025	PLGLB1	Cis_1M	lymphoblastoid	RTeQTL
rs11901025	AC125232.1	cis	Skin Sun Exposed Lower leg	GTEx
rs11901025	AC125232.1	cis	Whole Blood	GTEx
rs11901025	AC125232.1	cis	Nerve Tibial	GTEx
rs11901025	AC125232.1	cis	Esophagus Muscularis	GTEx
rs11901025	PLGLB2	cis	Artery Tibial	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:87258800-87283200	Weak transcription	Fetal Intestine Small	intestine
2	chr2:87259200-87281600	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:87268600-87280600	Weak transcription	Colonic Mucosa	Colon
4	chr2:87271800-87282200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr2:87275200-87281000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr2:87275200-87283000	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:87275600-87284000	Weak transcription	Fetal Stomach	stomach
8	chr2:87275600-87302000	Weak transcription	Duodenum Mucosa	Duodenum
9	chr2:87276000-87280800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:87276000-87281400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr2:87276200-87278800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:87276200-87285200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:87276400-87278800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:87276400-87282400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr2:87276400-87283400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:87276400-87283800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:87276400-87285000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:87276400-87295400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr2:87276400-87295400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:87276600-87283000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:87276600-87302000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr2:87276800-87279400	Weak transcription	Hela-S3	cervix
23	chr2:87277000-87281000	Weak transcription	Brain Germinal Matrix	brain
24	chr2:87277200-87279200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:87277200-87279200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:87277200-87279200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:87277200-87279200	Strong transcription	Fetal Thymus	thymus
28	chr2:87277200-87279800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:87277200-87284800	Weak transcription	Thymus	Thymus
30	chr2:87277400-87279200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:87277400-87279200	Strong transcription	Dnd41	blood
32	chr2:87277600-87279000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:87277600-87280600	Weak transcription	Fetal Lung	lung
34	chr2:87277800-87280400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:87277800-87287400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:87278000-87279400	Weak transcription	Left Ventricle	heart
37	chr2:87278000-87283800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr2:87278600-87279200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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