Variant report

Variant	rs1792165
Chromosome Location	chr11:73548270-73548271
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73547802..73550044-chr11:73567818..73570244,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10793066	0.84[CHB][hapmap]
rs10793067	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[LWK][hapmap]
rs10898931	0.86[CHB][hapmap]
rs10898935	0.86[CHB][hapmap]
rs10898946	0.92[ASN][1000 genomes]
rs11235876	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs12420357	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs1614987	0.81[ASN][1000 genomes]
rs1632159	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs1670537	0.86[CHB][hapmap];0.87[CHD][hapmap];0.91[LWK][hapmap];0.86[ASN][1000 genomes]
rs1670540	0.86[ASN][1000 genomes]
rs1670543	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[ASN][1000 genomes]
rs1670549	0.84[ASN][1000 genomes]
rs1670557	1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[LWK][hapmap];0.92[ASN][1000 genomes]
rs1670559	0.92[ASN][1000 genomes]
rs1670562	0.86[ASN][1000 genomes]
rs1670564	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs1670565	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs1670570	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1670572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1723835	0.82[ASN][1000 genomes]
rs1723843	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs1723848	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs1792156	0.86[CHB][hapmap];0.87[CHD][hapmap];0.91[LWK][hapmap];0.85[ASN][1000 genomes]
rs1792160	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs1792161	0.85[ASN][1000 genomes]
rs1792174	0.86[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs1792176	0.83[ASN][1000 genomes]
rs1792180	0.82[ASN][1000 genomes]
rs1792183	0.92[ASN][1000 genomes]
rs1792184	0.92[ASN][1000 genomes]
rs1792193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792198	1.00[CHB][hapmap];0.91[CHD][hapmap];0.82[LWK][hapmap];0.86[ASN][1000 genomes]
rs2140893	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs2444601	0.81[ASN][1000 genomes]
rs2444603	0.86[ASN][1000 genomes]
rs2444606	0.90[ASN][1000 genomes]
rs2462621	0.81[ASN][1000 genomes]
rs2511261	0.82[ASN][1000 genomes]
rs2511271	0.84[ASN][1000 genomes]
rs2511272	0.86[ASN][1000 genomes]
rs2512625	0.82[ASN][1000 genomes]
rs2512628	0.82[ASN][1000 genomes]
rs2512629	0.82[ASN][1000 genomes]
rs2515093	0.86[ASN][1000 genomes]
rs4471449	0.81[ASN][1000 genomes]
rs4514449	0.82[ASN][1000 genomes]
rs4558190	0.82[ASN][1000 genomes]
rs612914	0.80[CHB][hapmap]
rs653263	0.80[CHB][hapmap]
rs7119055	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs7934784	0.80[ASN][1000 genomes]
rs7940132	0.82[ASN][1000 genomes]
rs868667	0.86[CHB][hapmap];0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv1045149	chr11:73314565-73581908	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv530641	chr11:73358393-73638725	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1792165	RNF121	cis	cerebellum	SCAN
rs1792165	WDR71	cis	multi-tissue	Pritchard
rs1792165	MRPL48	cis	cerebellum	SCAN
rs1792165	PAAF1	cis	Lymphoblastoid	GTEx
rs1792165	PAAF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73499600-73549600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:73499600-73583800	Weak transcription	Aorta	Aorta
3	chr11:73500200-73574200	Weak transcription	Right Ventricle	heart
4	chr11:73500400-73571400	Weak transcription	Fetal Brain Male	brain
5	chr11:73500400-73583800	Weak transcription	Colonic Mucosa	Colon
6	chr11:73500600-73549200	Weak transcription	Osteobl	bone
7	chr11:73500600-73553800	Weak transcription	Fetal Lung	lung
8	chr11:73500800-73558800	Weak transcription	NHEK	skin
9	chr11:73508400-73570600	Weak transcription	Psoas Muscle	Psoas
10	chr11:73508800-73565000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:73508800-73573800	Weak transcription	Spleen	Spleen
12	chr11:73508800-73575400	Weak transcription	Gastric	stomach
13	chr11:73509000-73549400	Weak transcription	Brain Substantia Nigra	brain
14	chr11:73509000-73549600	Weak transcription	Brain Angular Gyrus	brain
15	chr11:73509000-73553200	Weak transcription	Lung	lung
16	chr11:73516000-73553200	Weak transcription	HepG2	liver
17	chr11:73517000-73562800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr11:73517000-73565200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:73517600-73549400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr11:73518400-73584000	Weak transcription	Pancreas	Pancrea
21	chr11:73522400-73549400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr11:73522400-73549400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr11:73525600-73549000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:73529800-73549200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr11:73530000-73549600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:73530400-73549400	Weak transcription	HSMM	muscle
27	chr11:73530600-73549200	Weak transcription	NH-A	brain
28	chr11:73530600-73549400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr11:73530600-73549600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr11:73530800-73549200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr11:73531000-73549200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:73531000-73549600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr11:73531800-73555600	Weak transcription	Fetal Kidney	kidney
34	chr11:73532000-73549400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:73532800-73548400	Weak transcription	Fetal Heart	heart
36	chr11:73533000-73580400	Weak transcription	Stomach Mucosa	stomach
37	chr11:73534400-73549200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr11:73534600-73549400	Weak transcription	A549	lung
39	chr11:73535200-73549600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr11:73535600-73549600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:73537200-73559800	Weak transcription	Small Intestine	intestine
42	chr11:73537400-73582600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr11:73538600-73549600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr11:73539000-73549200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:73539000-73577200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr11:73539200-73549400	Weak transcription	Brain Hippocampus Middle	brain
47	chr11:73539200-73574200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:73539200-73583800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr11:73539800-73549600	Weak transcription	Ovary	ovary
50	chr11:73540000-73549200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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