Variant report

Variant	rs3751000
Chromosome Location	chr11:9801925-9801926
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SWAP70-1	chr11:9801923-9802122	ENSG00000246273
2	lnc-SWAP70-1	chr11:9801923-9802122	ENSG00000246273
3	lnc-SWAP70-1	chr11:9801923-9802378	ENSG00000246273
4	lnc-SWAP70-1	chr11:9801923-9802052	NONHSAT017945
5	lnc-SWAP70-1	chr11:9800906-9802122	NONHSAT017946

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1032550	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10770060	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10770064	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10770065	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10840305	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10840306	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11042493	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12788348	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1875029	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1875030	0.85[EUR][1000 genomes]
rs1983002	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1996794	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34328537	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34690050	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35401279	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs360136	1.00[JPT][hapmap]
rs360137	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs360147	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs360157	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs415895	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs429835	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs440377	0.85[ASN][1000 genomes]
rs4910063	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4910499	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7126913	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7934930	0.89[ASN][1000 genomes]
rs7935673	0.90[ASN][1000 genomes]
rs960909	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3751000	OR52E6	cis	parietal	SCAN
rs3751000	ILK	cis	cerebellum	SCAN
rs3751000	SWAP70	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9780600-9813200	Weak transcription	Small Intestine	intestine
2	chr11:9781600-9809000	Weak transcription	Fetal Brain Male	brain
3	chr11:9787800-9805200	Weak transcription	Colonic Mucosa	Colon
4	chr11:9795200-9812800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr11:9796800-9803600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr11:9797200-9802000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:9797400-9821800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr11:9797600-9803600	Strong transcription	Fetal Intestine Large	intestine
9	chr11:9797800-9811800	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr11:9798000-9809000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:9798200-9805200	Weak transcription	Fetal Heart	heart
12	chr11:9798200-9810400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr11:9798400-9803600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:9798400-9805200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr11:9798600-9811600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:9798800-9803800	Strong transcription	Brain Germinal Matrix	brain
17	chr11:9798800-9805000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:9799000-9803400	Strong transcription	NH-A	brain
19	chr11:9799000-9803600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:9799000-9803600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr11:9799000-9803800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr11:9799000-9803800	Strong transcription	Osteobl	bone
23	chr11:9799000-9804000	Strong transcription	NHLF	lung
24	chr11:9799000-9806200	Strong transcription	Fetal Muscle Leg	muscle
25	chr11:9799000-9809200	Strong transcription	Fetal Stomach	stomach
26	chr11:9799200-9803200	Strong transcription	Primary hematopoietic stem cells	blood
27	chr11:9799200-9803200	Strong transcription	NHEK	skin
28	chr11:9799200-9803600	Strong transcription	Fetal Kidney	kidney
29	chr11:9799200-9803800	Strong transcription	Fetal Lung	lung
30	chr11:9799200-9803800	Strong transcription	Stomach Smooth Muscle	stomach
31	chr11:9799200-9806200	Strong transcription	Adipose Nuclei	Adipose
32	chr11:9799200-9812000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:9799200-9812200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:9799400-9803600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:9799400-9803600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:9799400-9803600	Strong transcription	NHDF-Ad	bronchial
37	chr11:9799600-9805400	Weak transcription	Right Atrium	heart
38	chr11:9799600-9806200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:9799600-9810600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr11:9799600-9823400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr11:9799800-9803600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr11:9799800-9811600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr11:9799800-9812000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr11:9799800-9812200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr11:9799800-9812200	Strong transcription	Liver	Liver
46	chr11:9799800-9814200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:9800000-9803800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr11:9800000-9805000	Strong transcription	Left Ventricle	heart
49	chr11:9800000-9807000	Strong transcription	Ovary	ovary
50	chr11:9800200-9805600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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