Variant report

Variant	rs12509847
Chromosome Location	chr4:78804237-78804238
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78783315..78786116-chr4:78803157..78806156,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169288	Chromatin interaction
ENSG00000250214	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10005531	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10005935	0.88[ASW][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap]
rs10018117	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10019920	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10026176	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10027634	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10027739	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs10030568	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs10049674	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1106457	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs11737353	0.85[YRI][hapmap]
rs11737861	0.82[YRI][hapmap]
rs11931686	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11942975	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13131331	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1587563	0.88[ASW][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.93[LWK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs17002804	0.85[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs1996740	0.84[MEX][hapmap]
rs2036455	0.88[CEU][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs2036457	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs28436599	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28685099	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4128860	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4328941	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4388114	0.82[LWK][hapmap];0.89[YRI][hapmap]
rs4410552	0.82[YRI][hapmap]
rs4859512	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4859513	0.96[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4859882	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859884	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4859890	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6533225	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs6533355	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6533372	0.80[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs67814821	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6811439	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6814088	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6816134	0.81[AFR][1000 genomes]
rs6820725	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6827822	0.82[YRI][hapmap]
rs6835993	0.80[CHB][hapmap]
rs6849145	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7436080	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs7660788	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7661064	0.82[YRI][hapmap]
rs7671941	0.82[YRI][hapmap]
rs7682450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7687812	0.82[LWK][hapmap];0.89[YRI][hapmap]
rs873280	0.88[CEU][hapmap];0.95[JPT][hapmap]
rs924684	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs924685	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9654194	0.88[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9994366	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv1824966	chr4:78747771-78823070	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1008217	chr4:78777531-78957311	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv537145	chr4:78777531-78957311	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription 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 miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12509847	BTC	cis	parietal	SCAN
rs12509847	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78784800-78808400	Weak transcription	Brain Substantia Nigra	brain
2	chr4:78784800-78842200	Weak transcription	HSMMtube	muscle
3	chr4:78784800-78859800	Weak transcription	Esophagus	oesophagus
4	chr4:78785000-78805800	Weak transcription	Colonic Mucosa	Colon
5	chr4:78785000-78807000	Weak transcription	Brain Anterior Caudate	brain
6	chr4:78785000-78808400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:78785000-78808800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:78785000-78810600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:78785000-78831200	Weak transcription	Brain Angular Gyrus	brain
10	chr4:78785000-78831600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr4:78785000-78841800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:78785000-78874400	Weak transcription	Right Ventricle	heart
13	chr4:78785200-78805000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:78785200-78806600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:78785200-78808400	Weak transcription	Fetal Brain Male	brain
16	chr4:78785200-78816200	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr4:78785200-78818800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr4:78785200-78820800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr4:78785400-78808200	Weak transcription	Fetal Kidney	kidney
20	chr4:78785400-78829800	Weak transcription	Fetal Heart	heart
21	chr4:78785600-78808200	Weak transcription	Hela-S3	cervix
22	chr4:78785600-78808400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr4:78790400-78808200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr4:78790400-78808400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr4:78790600-78843400	Weak transcription	Small Intestine	intestine
26	chr4:78790800-78817400	Weak transcription	NH-A	brain
27	chr4:78791400-78808000	Weak transcription	Ovary	ovary
28	chr4:78793600-78809400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:78794000-78851200	Weak transcription	Spleen	Spleen
30	chr4:78794200-78815600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:78794200-78851800	Weak transcription	Lung	lung
32	chr4:78795000-78805400	Weak transcription	Brain Hippocampus Middle	brain
33	chr4:78795000-78805600	Weak transcription	HUVEC	blood vessel
34	chr4:78795200-78805600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr4:78795200-78807000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:78795200-78808200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr4:78795400-78804800	Weak transcription	Left Ventricle	heart
38	chr4:78795600-78804800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr4:78795600-78805600	Weak transcription	NHDF-Ad	bronchial
40	chr4:78795600-78814600	Weak transcription	HSMM	muscle
41	chr4:78795600-78831800	Weak transcription	NHLF	lung
42	chr4:78795600-78833000	Weak transcription	Brain Germinal Matrix	brain
43	chr4:78795800-78804400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr4:78795800-78808200	Weak transcription	Fetal Brain Female	brain
45	chr4:78795800-78808600	Weak transcription	Fetal Lung	lung
46	chr4:78795800-78809200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr4:78796000-78804800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr4:78796000-78805600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:78796400-78805600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr4:78796600-78808400	Weak transcription	Colon Smooth Muscle	Colon

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