Variant report

Variant	rs12707772
Chromosome Location	chr8:103276753-103276754
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:103276020..103278945-chr8:103817511..103820437,2	MCF-7	breast:
2	chr8:103270085..103274841-chr8:103276076..103281465,7	K562	blood:
3	chr8:103275179..103277298-chr8:103288738..103290361,2	K562	blood:
4	chr8:103269135..103271624-chr8:103276230..103279592,4	MCF-7	breast:
5	chr8:103264839..103268068-chr8:103274584..103278724,3	MCF-7	breast:
6	chr8:103273449..103276603-chr8:103276750..103279820,3	K562	blood:
7	chr8:103276118..103278228-chr8:103313370..103316352,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253669	Chromatin interaction
ENSG00000104517	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10090707	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs10091086	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10099641	1.00[CHB][hapmap]
rs10102559	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10103923	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10108510	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap]
rs10108699	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10112713	1.00[CHB][hapmap]
rs10441502	0.83[ASN][1000 genomes]
rs10481100	1.00[CHB][hapmap]
rs10481101	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10505020	0.93[CEU][hapmap]
rs12114813	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap]
rs12335330	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap]
rs13248603	0.93[CEU][hapmap]
rs13249865	0.93[CEU][hapmap]
rs13250998	0.93[CEU][hapmap]
rs13258207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13259151	0.82[AMR][1000 genomes]
rs13261528	0.81[EUR][1000 genomes]
rs13262662	0.82[EUR][1000 genomes]
rs13263132	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13267556	1.00[CHB][hapmap]
rs13269311	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13278798	0.93[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs13278875	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2061299	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs2168689	1.00[CHB][hapmap]
rs2293982	0.92[EUR][1000 genomes]
rs28421590	1.00[CHB][hapmap]
rs28498487	0.83[ASN][1000 genomes]
rs28657820	0.83[ASN][1000 genomes]
rs28928572	0.83[ASN][1000 genomes]
rs2925778	1.00[CHB][hapmap]
rs2925783	1.00[CHB][hapmap]
rs2925784	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2925785	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2925787	1.00[CHB][hapmap]
rs2925791	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2925792	0.83[ASN][1000 genomes]
rs2978424	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2978425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2978426	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2978432	1.00[CHB][hapmap]
rs3018507	1.00[CHB][hapmap]
rs3018536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3018537	1.00[CHB][hapmap]
rs3018542	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3018543	1.00[CHB][hapmap]
rs34279135	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34351006	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34356268	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35166521	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35316247	0.82[EUR][1000 genomes]
rs35558240	0.83[EUR][1000 genomes]
rs35558370	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35969173	0.81[EUR][1000 genomes]
rs35980679	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36178006	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4483125	0.93[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs56003023	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59572423	0.81[EUR][1000 genomes]
rs71518852	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7840202	1.00[CHB][hapmap]
rs9649999	1.00[CHB][hapmap]
rs9650000	0.93[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9650001	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9650002	0.93[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][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	nsv1020359	chr8:103109921-103318415	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1033829	chr8:103110057-103525696	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1021459	chr8:103163436-103401754	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv539701	chr8:103163436-103401754	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1025935	chr8:103199207-103468322	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1018990	chr8:103207922-103357742	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv539702	chr8:103207922-103357742	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1028890	chr8:103207922-103401754	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv891242	chr8:103210971-103282418	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
10	nsv891243	chr8:103219629-103292724	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS 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	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12707772	RIMS2	cis	cerebellum	SCAN
rs12707772	PIGY	trans	cerebellum	SCAN
rs12707772	ATP6V1C1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103252200-103292800	Weak transcription	Gastric	stomach
2	chr8:103252200-103318800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:103252400-103280200	Weak transcription	Aorta	Aorta
4	chr8:103252400-103292400	Weak transcription	Psoas Muscle	Psoas
5	chr8:103252600-103280000	Weak transcription	Fetal Brain Male	brain
6	chr8:103255200-103279800	Strong transcription	Primary B cells from cord blood	blood
7	chr8:103256000-103299000	Strong transcription	Primary B cells from peripheral blood	blood
8	chr8:103256000-103299000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr8:103256000-103299600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr8:103256200-103285000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr8:103256200-103299600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr8:103257400-103299400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr8:103262400-103299400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr8:103262600-103281600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr8:103262600-103288200	Strong transcription	GM12878-XiMat	blood
16	chr8:103262600-103299600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:103262600-103329800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr8:103262800-103285200	Strong transcription	NHDF-Ad	bronchial
19	chr8:103262800-103286800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr8:103262800-103296000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr8:103262800-103299600	Strong transcription	HSMM	muscle
22	chr8:103263000-103294000	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr8:103263000-103299000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr8:103263000-103299000	Strong transcription	Liver	Liver
25	chr8:103263000-103299000	Strong transcription	Fetal Thymus	thymus
26	chr8:103263200-103284000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr8:103263200-103286800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr8:103263200-103292800	Strong transcription	Placenta	Placenta
29	chr8:103263200-103298800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr8:103263400-103285000	Strong transcription	Adipose Nuclei	Adipose
31	chr8:103263400-103295600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr8:103263400-103298200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr8:103263400-103299000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr8:103263400-103299000	Strong transcription	Dnd41	blood
35	chr8:103263400-103327800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr8:103263400-103327800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr8:103263800-103284600	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr8:103263800-103285200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr8:103264000-103299000	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr8:103264200-103299000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr8:103264800-103298800	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr8:103265000-103280600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr8:103265000-103284400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr8:103265200-103284800	Strong transcription	Fetal Lung	lung
45	chr8:103265600-103285200	Strong transcription	NH-A	brain
46	chr8:103266200-103285200	Strong transcription	Brain Anterior Caudate	brain
47	chr8:103266200-103285600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr8:103266200-103299400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr8:103266800-103329000	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr8:103267400-103327800	Strong transcription	HUES48 Cell Line	embryonic stem cell

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