Variant report

Variant	rs2276138
Chromosome Location	chr11:66456387-66456388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66247121..66250078-chr11:66454971..66457807,2	MCF-7	breast:
2	chr11:66444530..66447369-chr11:66455344..66460090,5	K562	blood:

Variant related genes	Relation type
ENSG00000254986	Chromatin interaction
ENSG00000173914	Chromatin interaction
ENSG00000255517	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12417769	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12577111	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12804382	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12805133	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.96[ASN][1000 genomes]
rs1671062	0.86[JPT][hapmap]
rs1671063	0.81[JPT][hapmap]
rs1671064	0.83[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs1791684	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1815739	0.83[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs2513658	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs34900764	0.88[EUR][1000 genomes]
rs3741363	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs474602	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs477557	0.85[ASN][1000 genomes]
rs486584	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs4930387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4930391	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs498045	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs503250	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs508443	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs509556	0.83[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap]
rs535211	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs540874	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs543191	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs556759	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs560556	0.83[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs566673	0.85[CEU][hapmap]
rs569818	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs572846	0.83[ASW][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap]
rs577023	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs577335	1.00[CEU][hapmap];0.83[ASN][1000 genomes]
rs580910	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs594313	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs608248	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs618838	0.83[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs627330	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs6591221	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs677488	0.83[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap]
rs678397	0.83[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs692892	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap]
rs8432	0.86[JPT][hapmap];0.80[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	nsv518919	chr11:66409409-66468469	Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS 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
4	nsv897790	chr11:66414915-66626234	Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv897791	chr11:66442855-66533469	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv427891	chr11:66456140-66606701	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2276138	CTSF	cis	cerebellum	SCAN
rs2276138	CCS	cis	lymphoblastoid	seeQTL
rs2276138	YIF1A	cis	cerebellum	SCAN
rs2276138	CTSF	cis	parietal	SCAN
rs2276138	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs2276138	CCDC85B	cis	parietal	SCAN
rs2276138	CDC42EP2	cis	cerebellum	SCAN
rs2276138	CCS	cis	multi-tissue	Pritchard
rs2276138	TRMT112	cis	cerebellum	SCAN
rs2276138	ACTN3	cis	lymphoblastoid	seeQTL
rs2276138	ACTN3	cis	Muscle Skeletal	GTEx
rs2276138	BBS1	cis	cerebellum	SCAN
rs2276138	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs2276138	PRDX5	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66446000-66457400	Weak transcription	Gastric	stomach
2	chr11:66446200-66456800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr11:66446200-66457200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:66446200-66457800	Weak transcription	Brain Angular Gyrus	brain
5	chr11:66446200-66458800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:66446200-66461400	Weak transcription	K562	blood
7	chr11:66446200-66461800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr11:66446200-66465800	Weak transcription	A549	lung
9	chr11:66446200-66468000	Weak transcription	Lung	lung
10	chr11:66446200-66468600	Weak transcription	Right Ventricle	heart
11	chr11:66446200-66480200	Weak transcription	Fetal Kidney	kidney
12	chr11:66446200-66485800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:66446400-66457400	Weak transcription	Brain Hippocampus Middle	brain
14	chr11:66446400-66462400	Weak transcription	Fetal Intestine Large	intestine
15	chr11:66446600-66461800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr11:66446800-66462200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:66450800-66467000	Strong transcription	Fetal Brain Female	brain
18	chr11:66451000-66456600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:66451000-66462200	Strong transcription	Liver	Liver
20	chr11:66451000-66467000	Strong transcription	Brain Germinal Matrix	brain
21	chr11:66451200-66461800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr11:66451200-66462200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:66451400-66462400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:66451600-66462000	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr11:66451800-66462000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr11:66451800-66462000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr11:66452200-66461400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr11:66452200-66485600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr11:66452400-66461000	Strong transcription	H9 Cell Line	embryonic stem cell
30	chr11:66452400-66461800	Strong transcription	Hela-S3	cervix
31	chr11:66452600-66461400	Strong transcription	Fetal Stomach	stomach
32	chr11:66452600-66461600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr11:66452600-66462000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr11:66452800-66461600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr11:66452800-66473800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr11:66453000-66483400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr11:66453400-66461800	Strong transcription	Pancreas	Pancrea
38	chr11:66453600-66457600	Strong transcription	Fetal Intestine Small	intestine
39	chr11:66454000-66461800	Weak transcription	Spleen	Spleen
40	chr11:66454000-66462000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr11:66454000-66462400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr11:66454600-66457400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr11:66455000-66462400	Weak transcription	Thymus	Thymus
44	chr11:66455200-66461800	Weak transcription	NHEK	skin
45	chr11:66455200-66462000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:66455600-66460800	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr11:66455800-66456400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr11:66455800-66456400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:66455800-66456600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr11:66455800-66457800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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