Variant report

Variant	rs7123875
Chromosome Location	chr11:66239147-66239148
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	chr11:66205770..66207413-chr11:66238542..66240436,2	MCF-7	breast:
2	chr11:65189570..65191757-chr11:66239067..66241497,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174547	Chromatin interaction
ENSG00000245532	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11110	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1201433	0.83[EUR][1000 genomes]
rs1785640	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2242663	0.84[JPT][hapmap]
rs2282640	0.94[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2509565	0.87[EUR][1000 genomes]
rs2511220	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2511224	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2511225	0.94[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4930376	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs610293	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs7947391	0.83[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.82[YRI][hapmap]
rs7951189	0.94[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
2	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
3	nsv897772	chr11:66018155-66254085	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
4	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
5	nsv832193	chr11:66120339-66278805	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
6	nsv897786	chr11:66203025-66244015	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv468601	chr11:66234023-66296114	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv555224	chr11:66234023-66296114	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7123875	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs7123875	ZDHHC24	cis	cerebellum	SCAN
rs7123875	NDUFV1	cis	parietal	SCAN
rs7123875	ACTN3	cis	lymphoblastoid	seeQTL
rs7123875	BBS1	cis	cerebellum	SCAN
rs7123875	CDC42EP2	cis	cerebellum	SCAN
rs7123875	UNC93B1	cis	cerebellum	SCAN
rs7123875	ASRGL1	cis	cerebellum	SCAN
rs7123875	KLC2	cis	parietal	SCAN
rs7123875	SUV420H1	cis	cerebellum	SCAN
rs7123875	CST6	cis	cerebellum	SCAN
rs7123875	CCS	cis	cerebellum	SCAN
rs7123875	POLR2G	cis	cerebellum	SCAN
rs7123875	ACTN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66235200-66239800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr11:66235200-66245000	Weak transcription	HSMM	muscle
3	chr11:66235200-66246200	Weak transcription	Fetal Kidney	kidney
4	chr11:66235400-66239800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr11:66235400-66239800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr11:66235400-66246400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr11:66235400-66246600	Weak transcription	Fetal Heart	heart
8	chr11:66235400-66246600	Weak transcription	Psoas Muscle	Psoas
9	chr11:66235400-66246600	Weak transcription	HSMMtube	muscle
10	chr11:66235600-66240000	Weak transcription	Osteobl	bone
11	chr11:66235600-66241400	Weak transcription	HMEC	breast
12	chr11:66235600-66244200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:66235600-66246400	Weak transcription	A549	lung
14	chr11:66235600-66246400	Weak transcription	Hela-S3	cervix
15	chr11:66235800-66239400	Weak transcription	NHDF-Ad	bronchial
16	chr11:66235800-66239600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:66235800-66239600	Weak transcription	Esophagus	oesophagus
18	chr11:66235800-66239600	Weak transcription	Fetal Intestine Large	intestine
19	chr11:66235800-66239600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:66235800-66239800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:66235800-66239800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:66235800-66239800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr11:66235800-66239800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:66235800-66239800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr11:66235800-66239800	Weak transcription	Colonic Mucosa	Colon
26	chr11:66235800-66239800	Weak transcription	Left Ventricle	heart
27	chr11:66235800-66239800	Weak transcription	Lung	lung
28	chr11:66235800-66240000	Weak transcription	Liver	Liver
29	chr11:66235800-66240600	Weak transcription	Right Ventricle	heart
30	chr11:66235800-66245000	Weak transcription	Thymus	Thymus
31	chr11:66235800-66246200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr11:66235800-66246200	Weak transcription	Fetal Thymus	thymus
33	chr11:66235800-66246400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr11:66235800-66246400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr11:66235800-66246600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:66235800-66246600	Weak transcription	Primary B cells from cord blood	blood
37	chr11:66235800-66246600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr11:66235800-66246600	Weak transcription	Stomach Mucosa	stomach
39	chr11:66236000-66239800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr11:66236000-66239800	Weak transcription	Pancreas	Pancrea
41	chr11:66236000-66240000	Weak transcription	Primary T cells from cord blood	blood
42	chr11:66236000-66241400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:66236000-66243800	Strong transcription	Brain Hippocampus Middle	brain
44	chr11:66236000-66244000	Strong transcription	Fetal Muscle Leg	muscle
45	chr11:66236000-66246200	Weak transcription	HepG2	liver
46	chr11:66236000-66246400	Weak transcription	Fetal Brain Male	brain
47	chr11:66236000-66246600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr11:66236000-66246600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr11:66236000-66246600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr11:66236000-66246600	Weak transcription	Rectal Mucosa Donor 31	rectum

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