Variant report

Variant	rs360124
Chromosome Location	chr11:9802228-9802229
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SWAP70-1	chr11:9801923-9802378	ENSG00000246273

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10118	0.84[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs10770062	0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1392026	0.93[ASN][1000 genomes]
rs183110	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1875030	0.90[ASN][1000 genomes]
rs2173030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645017	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2645029	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs360120	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs360127	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs360129	0.86[ASW][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs360130	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs360131	0.96[ASN][1000 genomes]
rs360132	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs360140	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs360141	0.92[ASN][1000 genomes]
rs360142	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360143	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360146	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs360150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs360151	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs360158	0.95[CHB][hapmap]
rs380806	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs391304	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs394315	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs405449	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs432849	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs438151	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs446760	0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs472487	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs634680	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6483726	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[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

No data

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	chr11:9797400-9821800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr11:9797600-9803600	Strong transcription	Fetal Intestine Large	intestine
8	chr11:9797800-9811800	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr11:9798000-9809000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr11:9798200-9805200	Weak transcription	Fetal Heart	heart
11	chr11:9798200-9810400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr11:9798400-9803600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr11:9798400-9805200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:9798600-9811600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr11:9798800-9803800	Strong transcription	Brain Germinal Matrix	brain
16	chr11:9798800-9805000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:9799000-9803400	Strong transcription	NH-A	brain
18	chr11:9799000-9803600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:9799000-9803600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr11:9799000-9803800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr11:9799000-9803800	Strong transcription	Osteobl	bone
22	chr11:9799000-9804000	Strong transcription	NHLF	lung
23	chr11:9799000-9806200	Strong transcription	Fetal Muscle Leg	muscle
24	chr11:9799000-9809200	Strong transcription	Fetal Stomach	stomach
25	chr11:9799200-9803200	Strong transcription	Primary hematopoietic stem cells	blood
26	chr11:9799200-9803200	Strong transcription	NHEK	skin
27	chr11:9799200-9803600	Strong transcription	Fetal Kidney	kidney
28	chr11:9799200-9803800	Strong transcription	Fetal Lung	lung
29	chr11:9799200-9803800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr11:9799200-9806200	Strong transcription	Adipose Nuclei	Adipose
31	chr11:9799200-9812000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:9799200-9812200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:9799400-9803600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:9799400-9803600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:9799400-9803600	Strong transcription	NHDF-Ad	bronchial
36	chr11:9799600-9805400	Weak transcription	Right Atrium	heart
37	chr11:9799600-9806200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr11:9799600-9810600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr11:9799600-9823400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr11:9799800-9803600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr11:9799800-9811600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr11:9799800-9812000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:9799800-9812200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr11:9799800-9812200	Strong transcription	Liver	Liver
45	chr11:9799800-9814200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr11:9800000-9803800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:9800000-9805000	Strong transcription	Left Ventricle	heart
48	chr11:9800000-9807000	Strong transcription	Ovary	ovary
49	chr11:9800200-9805600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:9800200-9823800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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