Variant report

Variant	rs1815739
Chromosome Location	chr11:66328095-66328096
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66327492..66329082-chr11:66331211..66334153,2	MCF-7	breast:
2	chr11:66311617..66317579-chr11:66325496..66333927,8	MCF-7	breast:
3	chr11:66327944..66330725-chr11:66391381..66393880,2	K562	blood:

Variant related genes	Relation type
ENSG00000174080	Chromatin interaction
ENSG00000248746	Chromatin interaction
ENSG00000174165	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10736656	0.85[ASN][1000 genomes]
rs10791882	0.94[ASN][1000 genomes]
rs1127894	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12577111	0.83[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]
rs12805133	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap]
rs1671062	0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs1671063	0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs1671064	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1671065	0.85[ASN][1000 genomes]
rs1700189	0.82[ASN][1000 genomes]
rs1791684	0.82[ASW][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs1791686	0.86[ASN][1000 genomes]
rs2000939	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276138	0.83[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs2279863	0.90[JPT][hapmap]
rs3018318	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3741363	0.83[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs474602	0.90[YRI][hapmap]
rs486584	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4930387	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs498045	0.80[GIH][hapmap]
rs503250	0.83[CHB][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.84[MKK][hapmap];0.90[YRI][hapmap];0.81[ASN][1000 genomes]
rs508443	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs509556	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs531490	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs535211	0.91[JPT][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];0.90[YRI][hapmap]
rs540874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs545009	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs556759	0.83[CHB][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.84[MKK][hapmap];0.90[YRI][hapmap];0.81[ASN][1000 genomes]
rs560556	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs566673	0.84[GIH][hapmap]
rs572846	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577023	0.80[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap]
rs580910	0.80[GIH][hapmap];0.91[JPT][hapmap]
rs615205	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs618838	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs630021	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs677488	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs678397	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs692892	0.83[CHB][hapmap];0.80[GIH][hapmap]
rs7925108	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs8432	0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.89[YRI][hapmap];0.86[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	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
2	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	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
4	nsv897787	chr11:66300348-66347850	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv897788	chr11:66319262-66347850	Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs1815739	CTSF	cis	brain	BrainEAC
rs1815739	UNC93B1	cis	cerebellum	SCAN
rs1815739	CTSF	cis	parietal	SCAN
rs1815739	ACTN3	cis	lymphoblastoid	seeQTL
rs1815739	PRDX5	cis	cerebellum	SCAN
rs1815739	ACTN3	cis	Muscle Skeletal	GTEx
rs1815739	CCDC85B	cis	parietal	SCAN
rs1815739	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs1815739	KDM2A	cis	cerebellum	SCAN
rs1815739	CTSF	cis	cerebellum	SCAN
rs1815739	YIF1A	cis	parietal	SCAN
rs1815739	CDC42EP2	cis	cerebellum	SCAN
rs1815739	GANAB	cis	parietal	SCAN
rs1815739	CCS	cis	lymphoblastoid	seeQTL
rs1815739	YIF1A	cis	cerebellum	SCAN
rs1815739	CCS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66319000-66337800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:66321400-66330400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:66321400-66331600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:66322600-66331400	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr11:66325000-66329200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:66326400-66328400	Enhancers	Spleen	Spleen
7	chr11:66326600-66329000	Weak transcription	Brain Angular Gyrus	brain
8	chr11:66326600-66329400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr11:66326600-66329600	Weak transcription	Brain Substantia Nigra	brain
10	chr11:66326600-66331800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr11:66326600-66334800	Weak transcription	Colon Smooth Muscle	Colon
12	chr11:66326800-66329400	Weak transcription	Adipose Nuclei	Adipose
13	chr11:66326800-66329800	Weak transcription	Brain Anterior Caudate	brain
14	chr11:66326800-66329800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:66326800-66329800	Weak transcription	Fetal Brain Female	brain
16	chr11:66326800-66331200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:66326800-66331200	Weak transcription	Right Ventricle	heart
18	chr11:66326800-66331400	Weak transcription	Liver	Liver
19	chr11:66326800-66334800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr11:66326800-66334800	Weak transcription	Pancreas	Pancrea
21	chr11:66326800-66335000	Weak transcription	Psoas Muscle	Psoas
22	chr11:66326800-66335000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr11:66326800-66335200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:66326800-66335200	Weak transcription	Esophagus	oesophagus
25	chr11:66326800-66335200	Weak transcription	Left Ventricle	heart
26	chr11:66326800-66335200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:66327000-66330400	Weak transcription	Ovary	ovary
28	chr11:66327000-66332600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr11:66327000-66333000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr11:66327000-66335200	Weak transcription	Fetal Heart	heart
31	chr11:66327200-66328200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr11:66327200-66328600	Weak transcription	K562	blood
33	chr11:66327200-66329000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr11:66327200-66329400	Weak transcription	Brain Germinal Matrix	brain
35	chr11:66327200-66329400	Weak transcription	Brain Hippocampus Middle	brain
36	chr11:66327200-66329600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr11:66327200-66330400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr11:66327200-66330800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr11:66327200-66332200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr11:66327200-66333200	Weak transcription	Lung	lung
41	chr11:66327200-66335000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr11:66327400-66329400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:66327400-66331800	Weak transcription	Placenta	Placenta
44	chr11:66327400-66334600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr11:66327400-66335200	Weak transcription	Right Atrium	heart
46	chr11:66327600-66330400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:66327600-66332200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr11:66327800-66328200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:66327800-66328200	Enhancers	Gastric	stomach
50	chr11:66327800-66328800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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