Variant report

Variant	rs56716157
Chromosome Location	chr8:95542872-95542873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:95539618..95543703-chr8:95563899..95568056,6	MCF-7	breast:
2	chr8:95521196..95523567-chr8:95542412..95544633,2	MCF-7	breast:
3	chr8:95536103..95541001-chr8:95541149..95546680,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164944	Chromatin interaction
ENSG00000253704	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10104041	0.86[ASN][1000 genomes]
rs10111287	0.86[ASN][1000 genomes]
rs1023767	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1048029	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1055800	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10956915	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10956919	0.84[ASN][1000 genomes]
rs11986009	0.86[ASN][1000 genomes]
rs11992893	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12540967	0.84[ASN][1000 genomes]
rs12541408	0.84[ASN][1000 genomes]
rs12543207	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12543730	0.84[ASN][1000 genomes]
rs12678305	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12679345	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12680842	0.84[ASN][1000 genomes]
rs12680855	0.84[ASN][1000 genomes]
rs12680965	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12681564	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1470153	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16916874	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16916881	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1992370	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2304764	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2381882	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2381885	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28729295	0.86[ASN][1000 genomes]
rs28817653	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4269508	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4366055	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4373498	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4735297	0.84[ASN][1000 genomes]
rs55897841	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56042558	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56302978	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60655325	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72674824	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72674832	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72674843	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72674852	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72674855	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72674861	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72674866	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72674867	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72674877	0.84[ASN][1000 genomes]
rs7829886	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs957447	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs957448	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv611750	chr8:95519205-95574634	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56716157	KIAA1429	cis	brain	BrainEAC
rs56716157	KIAA1429	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr8:95497200-95564200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr8:95498400-95554000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:95499400-95552200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr8:95516800-95554600	Strong transcription	Fetal Thymus	thymus
6	chr8:95520400-95555200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr8:95520600-95552400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr8:95527600-95548600	Strong transcription	Fetal Muscle Leg	muscle
9	chr8:95532800-95558800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr8:95534000-95543600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr8:95534200-95545000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr8:95535400-95556000	Weak transcription	Fetal Heart	heart
13	chr8:95535800-95549800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr8:95535800-95555600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr8:95536000-95555600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr8:95536200-95549200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr8:95536400-95552200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr8:95536600-95557000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr8:95536800-95543200	Strong transcription	Rectal Smooth Muscle	rectum
20	chr8:95536800-95543400	Strong transcription	Brain Germinal Matrix	brain
21	chr8:95536800-95546600	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr8:95536800-95549800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr8:95536800-95550600	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr8:95536800-95551400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr8:95536800-95552400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr8:95536800-95556600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr8:95537000-95543400	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr8:95537000-95543600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr8:95537000-95543600	Strong transcription	A549	lung
30	chr8:95537000-95544400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr8:95537000-95545200	Strong transcription	Fetal Brain Female	brain
32	chr8:95537000-95545200	Strong transcription	HepG2	liver
33	chr8:95537000-95547000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr8:95537000-95547800	Strong transcription	Brain Anterior Caudate	brain
35	chr8:95537000-95548000	Strong transcription	Thymus	Thymus
36	chr8:95537000-95548400	Strong transcription	Brain Hippocampus Middle	brain
37	chr8:95537000-95548400	Strong transcription	Hela-S3	cervix
38	chr8:95537000-95549000	Strong transcription	GM12878-XiMat	blood
39	chr8:95537000-95549400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr8:95537000-95550600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr8:95537000-95550600	Strong transcription	Fetal Lung	lung
42	chr8:95537000-95550800	Strong transcription	Dnd41	blood
43	chr8:95537000-95551000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr8:95537000-95552000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr8:95537000-95552200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr8:95537000-95552400	Strong transcription	Primary B cells from cord blood	blood
47	chr8:95537000-95552400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr8:95537000-95552400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr8:95537000-95552400	Strong transcription	Adipose Nuclei	Adipose
50	chr8:95537000-95552400	Strong transcription	Duodenum Mucosa	Duodenum

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