Variant report

Variant	rs12544329
Chromosome Location	chr8:48423840-48423841
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:48423448..48424045-chr8:48651002..48651682,2	MCF-7	breast:
2	chr8:48416787..48427648-chr8:48644938..48653304,27	MCF-7	breast:
3	chr8:48417772..48429044-chr8:48646094..48652486,42	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221869	Chromatin interaction
ENSG00000164808	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10094128	0.82[CEU][hapmap]
rs1038797	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10808752	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs10957549	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10957644	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10958058	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1106607	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11778548	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11781727	1.00[ASW][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap]
rs11782572	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11784823	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs12549996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12675378	0.98[EUR][1000 genomes]
rs12678110	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12682269	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs16928696	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1872840	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2087656	1.00[ASW][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.88[MKK][hapmap]
rs2129617	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2129618	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2130412	0.97[EUR][1000 genomes]
rs2130413	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2172121	1.00[ASW][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap]
rs4489323	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4536257	0.96[CEU][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs4594029	0.82[CEU][hapmap]
rs4608108	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4873102	0.89[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[MKK][hapmap]
rs4873368	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4873395	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4873399	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4873437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4873478	0.82[CEU][hapmap]
rs4873507	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4873529	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4873546	0.81[CEU][hapmap]
rs4873565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4873619	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55941013	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56092229	0.94[EUR][1000 genomes]
rs62539116	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62539144	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62539147	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62539150	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6982620	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6986054	0.82[CEU][hapmap]
rs6987043	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6989917	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6990123	1.00[ASW][hapmap];0.80[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.95[MKK][hapmap]
rs7826284	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7842068	0.82[CEU][hapmap]
rs876915	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs923499	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693377	chr8:47824261-48582964	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv491863	chr8:48053825-48586176	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1025674	chr8:48306843-48548862	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1023409	chr8:48320442-48454089	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv539595	chr8:48320442-48454089	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv890848	chr8:48405007-48535622	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv470211	chr8:48405007-48545961	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12544329	KIAA0146	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48397600-48426400	Weak transcription	Aorta	Aorta
2	chr8:48410600-48424000	Weak transcription	Brain Angular Gyrus	brain
3	chr8:48411600-48424000	Weak transcription	Fetal Kidney	kidney
4	chr8:48418400-48424600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:48418400-48436000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr8:48420200-48426400	Weak transcription	Esophagus	oesophagus
7	chr8:48420400-48425000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr8:48420600-48424000	Weak transcription	NH-A	brain
9	chr8:48420600-48424600	Weak transcription	HMEC	breast
10	chr8:48420600-48424800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr8:48420600-48425000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr8:48420800-48424200	Weak transcription	Colon Smooth Muscle	Colon
13	chr8:48420800-48424400	Weak transcription	Brain Anterior Caudate	brain
14	chr8:48420800-48424800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr8:48420800-48425400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr8:48420800-48426000	Weak transcription	Primary T cells from cord blood	blood
17	chr8:48421000-48424400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr8:48421000-48424800	Weak transcription	Stomach Mucosa	stomach
19	chr8:48421200-48424600	Weak transcription	NHEK	skin
20	chr8:48421200-48426000	Weak transcription	K562	blood
21	chr8:48421800-48424200	Strong transcription	Dnd41	blood
22	chr8:48421800-48424600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr8:48421800-48435200	Weak transcription	Primary B cells from cord blood	blood
24	chr8:48422000-48424200	Weak transcription	Fetal Intestine Large	intestine
25	chr8:48422000-48434800	Weak transcription	Fetal Thymus	thymus
26	chr8:48422200-48424000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr8:48422200-48424400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr8:48422200-48425000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr8:48422200-48425600	Weak transcription	Brain Hippocampus Middle	brain
30	chr8:48422400-48424600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr8:48422600-48424000	Weak transcription	Spleen	Spleen
32	chr8:48422600-48424400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr8:48422600-48424600	Weak transcription	Liver	Liver
34	chr8:48422600-48424600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr8:48422600-48424800	Enhancers	Fetal Lung	lung
36	chr8:48422600-48425600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr8:48422600-48425600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr8:48422600-48425600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr8:48422600-48425600	Weak transcription	GM12878-XiMat	blood
40	chr8:48422600-48426200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr8:48422600-48426200	Weak transcription	Fetal Brain Male	brain
42	chr8:48423000-48424600	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr8:48423200-48424600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr8:48423200-48425000	Enhancers	Lung	lung
45	chr8:48423200-48428400	Enhancers	Placenta	Placenta
46	chr8:48423400-48424000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr8:48423400-48424000	Strong transcription	Fetal Intestine Small	intestine
48	chr8:48423400-48424200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr8:48423400-48424200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr8:48423400-48424200	Genic enhancers	Fetal Muscle Trunk	muscle

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