Variant report

Variant	rs12681564
Chromosome Location	chr8:95513395-95513396
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	chr8:95512268..95514297-chr8:95730615..95733456,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156162	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10104041	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10111287	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1023767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1048029	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1055800	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10956915	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10956919	0.94[ASN][1000 genomes]
rs11986009	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11992893	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12540967	0.94[ASN][1000 genomes]
rs12541408	0.94[ASN][1000 genomes]
rs12543207	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12543730	0.94[ASN][1000 genomes]
rs12678305	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12679345	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12680842	0.93[ASN][1000 genomes]
rs12680855	0.93[ASN][1000 genomes]
rs12680965	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1470153	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16916874	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16916881	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1992370	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2304764	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2381882	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2381885	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28729295	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28817653	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4269508	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4366055	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4373498	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4735297	0.92[ASN][1000 genomes]
rs55897841	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56042558	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56302978	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56716157	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60655325	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72674824	0.81[ASN][1000 genomes]
rs72674832	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72674843	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72674852	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72674855	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72674861	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72674866	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72674867	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72674877	0.94[ASN][1000 genomes]
rs7829886	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs957447	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs957448	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv532338	chr8:95296118-95971825	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS 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	61 gene(s)	inside rSNPs	diseases
4	nsv429928	chr8:95488800-95672033	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12681564	KIAA1429	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:95493000-95549200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:95495200-95538400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr8:95495600-95541000	Weak transcription	Esophagus	oesophagus
4	chr8:95497200-95564200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr8:95498400-95554000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:95499200-95514400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr8:95499200-95515200	Strong transcription	Fetal Thymus	thymus
8	chr8:95499200-95519000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:95499200-95519000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr8:95499400-95514200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr8:95499400-95514400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr8:95499400-95519000	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr8:95499400-95519000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr8:95499400-95533400	Strong transcription	Placenta	Placenta
15	chr8:95499400-95552200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr8:95499600-95514600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr8:95499600-95515400	Strong transcription	Liver	Liver
18	chr8:95500200-95519000	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr8:95500400-95514000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr8:95500400-95514200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr8:95500400-95524600	Weak transcription	Stomach Mucosa	stomach
22	chr8:95501200-95541000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr8:95502600-95516800	Weak transcription	Fetal Heart	heart
24	chr8:95502600-95517200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr8:95502600-95517200	Weak transcription	Small Intestine	intestine
26	chr8:95503400-95517200	Weak transcription	Spleen	Spleen
27	chr8:95504000-95516400	Weak transcription	Right Ventricle	heart
28	chr8:95504000-95521800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr8:95504000-95522000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr8:95504200-95516600	Weak transcription	Fetal Brain Male	brain
31	chr8:95504400-95523400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr8:95505000-95517200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr8:95505400-95516200	Weak transcription	Brain Hippocampus Middle	brain
34	chr8:95505400-95517200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr8:95505600-95521600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr8:95506000-95522000	Weak transcription	HMEC	breast
37	chr8:95506400-95514600	Strong transcription	Thymus	Thymus
38	chr8:95506400-95516400	Weak transcription	Hela-S3	cervix
39	chr8:95506400-95516600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr8:95507400-95516400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr8:95508200-95517400	Weak transcription	Psoas Muscle	Psoas
42	chr8:95508400-95516400	Weak transcription	GM12878-XiMat	blood
43	chr8:95508600-95516600	Weak transcription	K562	blood
44	chr8:95508600-95518200	Weak transcription	Colon Smooth Muscle	Colon
45	chr8:95508800-95516400	Weak transcription	HSMMtube	muscle
46	chr8:95508800-95516600	Weak transcription	Brain Anterior Caudate	brain
47	chr8:95508800-95522600	Weak transcription	Brain Substantia Nigra	brain
48	chr8:95509000-95516800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr8:95509000-95522000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr8:95509200-95514600	Strong transcription	Fetal Intestine Small	intestine

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