Variant report

Variant	rs7947761
Chromosome Location	chr11:100624599-100624600
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	chr11:100512013..100514802-chr11:100624099..100626304,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242165	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11224405	0.82[ASN][1000 genomes]
rs11824393	0.82[ASN][1000 genomes]
rs11824432	0.82[ASN][1000 genomes]
rs12284151	0.82[ASN][1000 genomes]
rs17095405	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17095409	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17095426	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17095428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17095429	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17095438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17095439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2088953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3901516	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4087602	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4121392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4337001	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4469852	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4517481	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4753983	0.82[ASN][1000 genomes]
rs4754702	0.81[ASW][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap]
rs499241	0.81[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs507695	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs58727919	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60708905	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61890760	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61890763	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61890764	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61890765	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61890766	0.88[ASN][1000 genomes]
rs61892334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61892352	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61892355	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61910476	0.88[ASN][1000 genomes]
rs61910478	0.82[ASN][1000 genomes]
rs61910480	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs61910505	0.82[ASN][1000 genomes]
rs61910508	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6590818	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7102634	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7105842	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7110872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7112228	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7112366	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7116153	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7120712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7126015	0.82[ASN][1000 genomes]
rs7126324	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130855	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73003836	0.82[ASN][1000 genomes]
rs73005729	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7927197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7942588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7944598	0.88[EUR][1000 genomes]
rs7945336	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053430	chr11:99888390-100629136	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1042067	chr11:99889697-100629136	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1037689	chr11:99895378-100624599	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1040942	chr11:99895378-100629136	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1045190	chr11:99913193-100627395	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv541153	chr11:99913193-100627395	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv529454	chr11:99913394-100627255	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv520995	chr11:100163957-100681211	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv530643	chr11:100196082-100713156	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv898327	chr11:100569021-100631075	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7947761	TMEM123	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:100612400-100630800	Weak transcription	Right Atrium	heart
2	chr11:100613000-100631600	Weak transcription	Ovary	ovary
3	chr11:100613200-100628400	Weak transcription	Fetal Kidney	kidney
4	chr11:100620800-100626800	Weak transcription	Liver	Liver
5	chr11:100620800-100628400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr11:100621000-100642400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr11:100621400-100631600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:100622200-100625800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr11:100622800-100624600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:100622800-100624600	Enhancers	Placenta	Placenta
11	chr11:100622800-100624800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr11:100622800-100624800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr11:100622800-100624800	Enhancers	HMEC	breast
14	chr11:100622800-100624800	Enhancers	NHEK	skin
15	chr11:100622800-100625200	Enhancers	Fetal Heart	heart
16	chr11:100623000-100624600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:100623000-100624600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:100623000-100624600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr11:100623000-100624800	Enhancers	Stomach Mucosa	stomach
20	chr11:100623000-100625000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr11:100623000-100625200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr11:100623000-100625200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr11:100623000-100625200	Enhancers	A549	lung
24	chr11:100623000-100626000	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr11:100623000-100626400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:100623200-100624600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:100623200-100624600	Enhancers	Left Ventricle	heart
28	chr11:100623200-100624600	Enhancers	Right Ventricle	heart
29	chr11:100623200-100624800	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr11:100623200-100625000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:100623200-100625400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr11:100623200-100626000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr11:100623200-100626400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr11:100623400-100624600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:100623400-100624800	Enhancers	H9 Cell Line	embryonic stem cell
36	chr11:100623400-100624800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr11:100623400-100625000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr11:100623400-100625400	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr11:100623400-100632000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:100623600-100624600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr11:100623600-100624600	Enhancers	Hela-S3	cervix
42	chr11:100623600-100624800	Enhancers	Fetal Muscle Leg	muscle
43	chr11:100623600-100625000	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr11:100623600-100625400	Enhancers	Duodenum Mucosa	Duodenum
45	chr11:100623800-100624600	Enhancers	Adipose Nuclei	Adipose
46	chr11:100623800-100624800	Enhancers	Fetal Intestine Large	intestine
47	chr11:100623800-100625200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr11:100623800-100625200	Enhancers	Fetal Intestine Small	intestine
49	chr11:100624000-100624600	Enhancers	Brain Substantia Nigra	brain
50	chr11:100624000-100624800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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