Variant report

Variant	rs2248540
Chromosome Location	chr11:120426966-120426967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10892587	0.89[ASN][1000 genomes]
rs1320718	0.86[ASN][1000 genomes]
rs1320720	0.85[ASN][1000 genomes]
rs2252244	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2252385	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2266133	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2508652	0.80[AMR][1000 genomes]
rs2508655	0.84[AMR][1000 genomes]
rs3901366	0.83[AMR][1000 genomes]
rs4272790	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs4310631	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs4363614	0.87[ASN][1000 genomes]
rs4938817	0.86[ASN][1000 genomes]
rs7950360	0.83[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	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1051115	chr11:120376808-120446434	Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1036388	chr11:120395104-120427135	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1054301	chr11:120396485-120465800	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1035499	chr11:120398643-120446434	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1049494	chr11:120400115-120453381	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1052932	chr11:120406628-120442955	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2248540	PVRL1	cis	parietal	SCAN
rs2248540	C1QTNF5	cis	parietal	SCAN
rs2248540	DPAGT1	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120419800-120429600	Weak transcription	Right Ventricle	heart
2	chr11:120419800-120433600	Weak transcription	Right Atrium	heart
3	chr11:120424000-120428200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr11:120424600-120433600	Weak transcription	Left Ventricle	heart
5	chr11:120425200-120427800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:120425200-120428200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:120425400-120427000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr11:120425400-120428200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:120425600-120427000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
10	chr11:120425600-120427000	Enhancers	Fetal Brain Male	brain
11	chr11:120425600-120427000	Enhancers	Fetal Kidney	kidney
12	chr11:120425600-120427000	Enhancers	Fetal Lung	lung
13	chr11:120425600-120427200	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr11:120425600-120427400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:120425600-120427400	Enhancers	GM12878-XiMat	blood
16	chr11:120425600-120428200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:120425600-120428200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:120425600-120428200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:120425800-120427000	Enhancers	Brain Anterior Caudate	brain
20	chr11:120425800-120427400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:120425800-120428000	Enhancers	Primary B cells from peripheral blood	blood
22	chr11:120425800-120428200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
23	chr11:120426200-120427000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:120426200-120427200	Weak transcription	Fetal Brain Female	brain
25	chr11:120426400-120428200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
26	chr11:120426400-120428200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
27	chr11:120426600-120427000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr11:120426600-120427000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:120426600-120427600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr11:120426600-120427800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:120426600-120432600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:120426600-120432800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr11:120426600-120433400	Weak transcription	Brain Substantia Nigra	brain
34	chr11:120426800-120427200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr11:120426800-120429600	Weak transcription	Brain Hippocampus Middle	brain
36	chr11:120426800-120429800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr11:120426800-120433600	Weak transcription	Brain Inferior Temporal Lobe	brain

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