Variant report

Variant	rs615304
Chromosome Location	chr11:86969997-86969998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FZD4-8	chr11:86969893-86970301	NONHSAT023515

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs214743	0.84[AFR][1000 genomes]
rs2678818	0.81[AFR][1000 genomes]
rs301582	0.93[ASW][hapmap];0.85[LWK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs301600	0.80[AFR][1000 genomes]
rs301605	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs525949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533510	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577675	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647149	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037042	chr11:86586876-86978492	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv541119	chr11:86586876-86978492	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1043562	chr11:86755535-87547185	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv541120	chr11:86755535-87547185	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1046288	chr11:86757573-87158571	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv1045057	chr11:86794670-87033779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541121	chr11:86794670-87033779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv468777	chr11:86794856-86985581	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv555707	chr11:86794856-86985581	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv468778	chr11:86850483-86974576	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv555708	chr11:86850483-86974576	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv898064	chr11:86864277-87013438	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv2829956	chr11:86872504-87025059	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv898065	chr11:86891077-86984439	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv898066	chr11:86891077-86989134	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv468779	chr11:86928253-87001892	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv555709	chr11:86928253-87001892	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv898068	chr11:86930270-87005969	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
19	nsv898069	chr11:86932603-86984439	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
20	nsv898070	chr11:86932603-86989134	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
21	nsv555710	chr11:86947024-87001892	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
22	nsv555711	chr11:86960516-87001892	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
23	nsv555712	chr11:86961994-87007030	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
24	nsv898071	chr11:86963330-87001892	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
25	nsv898072	chr11:86963330-87005969	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
26	nsv898073	chr11:86963330-87013438	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
27	nsv898074	chr11:86963330-87034696	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs615304	PICALM	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86962400-86972000	Weak transcription	Primary T cells from cord blood	blood
2	chr11:86962800-86977600	Weak transcription	K562	blood
3	chr11:86963000-86976200	Weak transcription	Colon Smooth Muscle	Colon
4	chr11:86964400-86970800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:86964600-86970800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:86966600-86970400	Weak transcription	Pancreas	Pancrea
7	chr11:86966800-86970800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr11:86967000-86975400	Weak transcription	HepG2	liver
9	chr11:86968000-86970000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:86968000-86971400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr11:86968200-86971800	Weak transcription	Osteobl	bone
12	chr11:86968400-86972000	Weak transcription	NHDF-Ad	bronchial
13	chr11:86968800-86970400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr11:86968800-86971000	Weak transcription	Fetal Lung	lung
15	chr11:86969200-86972200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:86969400-86970000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:86969400-86970200	Enhancers	Adipose Nuclei	Adipose
18	chr11:86969400-86970200	Enhancers	Right Atrium	heart
19	chr11:86969400-86970400	Enhancers	Primary hematopoietic stem cells	blood
20	chr11:86969400-86970400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr11:86969400-86970400	Enhancers	Left Ventricle	heart
22	chr11:86969400-86970400	Enhancers	Lung	lung
23	chr11:86969400-86971200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr11:86969400-86971400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:86969400-86972000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:86969600-86970200	Weak transcription	Aorta	Aorta
27	chr11:86969600-86972800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr11:86969600-86976000	Weak transcription	Fetal Kidney	kidney
29	chr11:86969800-86970000	Weak transcription	Fetal Stomach	stomach
30	chr11:86969800-86970800	Weak transcription	Brain Angular Gyrus	brain
31	chr11:86969800-86970800	Weak transcription	HUVEC	blood vessel
32	chr11:86969800-86971600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr11:86969800-86972200	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr11:86969800-86995400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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