Variant report

Variant	rs532439
Chromosome Location	chr11:66469032-66469033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12795774	0.90[CEU][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs1987169	0.81[EUR][1000 genomes]
rs481296	0.90[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap]
rs484262	0.90[CEU][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs508996	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs551708	0.86[GIH][hapmap]
rs624561	0.90[CEU][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv897791	chr11:66442855-66533469	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv427891	chr11:66456140-66606701	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv468602	chr11:66468469-66634397	Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv555225	chr11:66468469-66634397	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs532439	FERMT3	cis	cerebellum	SCAN
rs532439	CCS	cis	lymphoblastoid	seeQTL
rs532439	RBM14	cis	multi-tissue	Pritchard
rs532439	NXF1	cis	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66446200-66480200	Weak transcription	Fetal Kidney	kidney
2	chr11:66446200-66485800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr11:66452200-66485600	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr11:66452800-66473800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr11:66453000-66483400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr11:66456400-66494600	Weak transcription	Right Atrium	heart
7	chr11:66458600-66469200	Strong transcription	Placenta Amnion	Placenta Amnion
8	chr11:66459000-66472200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr11:66462600-66484000	Weak transcription	Brain Substantia Nigra	brain
10	chr11:66462800-66472200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:66462800-66481000	Weak transcription	HMEC	breast
12	chr11:66462800-66484400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:66463000-66469600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:66463000-66472000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:66463000-66485000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr11:66463200-66470200	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr11:66463400-66469400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:66463400-66470200	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:66463400-66471800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:66463600-66469400	Strong transcription	Pancreas	Pancrea
21	chr11:66463600-66469600	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr11:66463600-66469800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr11:66463600-66470000	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr11:66463600-66470000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr11:66463800-66469600	Strong transcription	Brain Angular Gyrus	brain
26	chr11:66464400-66469600	Strong transcription	Brain Anterior Caudate	brain
27	chr11:66465000-66469600	Strong transcription	NHEK	skin
28	chr11:66465000-66470200	Strong transcription	Hela-S3	cervix
29	chr11:66465200-66469200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr11:66465200-66469400	Strong transcription	Brain Hippocampus Middle	brain
31	chr11:66465400-66471800	Weak transcription	Thymus	Thymus
32	chr11:66465600-66487000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr11:66465800-66469600	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr11:66465800-66469600	Strong transcription	A549	lung
35	chr11:66465800-66480200	Weak transcription	Fetal Brain Male	brain
36	chr11:66466400-66469200	Strong transcription	Esophagus	oesophagus
37	chr11:66467000-66469400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:66467200-66480200	Weak transcription	Ovary	ovary
39	chr11:66467400-66469200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:66467400-66485200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr11:66467600-66470200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:66467800-66469200	Genic enhancers	Liver	Liver
43	chr11:66467800-66469400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:66467800-66469400	Strong transcription	Gastric	stomach
45	chr11:66467800-66469600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr11:66467800-66469800	Enhancers	Primary hematopoietic stem cells	blood
47	chr11:66468000-66480400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:66468200-66469400	Strong transcription	Fetal Intestine Small	intestine
49	chr11:66468200-66469600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:66468200-66474600	Weak transcription	Fetal Muscle Leg	muscle

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