Variant report

Variant	rs2172121
Chromosome Location	chr8:48291480-48291481
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:48276921..48279533-chr8:48290586..48293171,2	MCF-7	breast:
2	chr8:48286201..48287772-chr8:48290885..48293117,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1038797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10808752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10957074	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1106607	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11774001	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11775514	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11775628	0.93[EUR][1000 genomes]
rs11779423	0.80[EUR][1000 genomes]
rs11781727	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11782572	1.00[ASW][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap]
rs11782728	0.82[AMR][1000 genomes]
rs11783141	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11785228	0.99[EUR][1000 genomes]
rs12541086	1.00[CEU][hapmap];0.84[CHD][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs12543823	0.94[EUR][1000 genomes]
rs12544329	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]
rs12547513	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12549996	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12680669	0.98[EUR][1000 genomes]
rs12682269	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13259872	0.81[EUR][1000 genomes]
rs13259913	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2087656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2130879	0.92[EUR][1000 genomes]
rs2362554	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs34099416	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs35045730	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35235599	0.83[EUR][1000 genomes]
rs4242439	0.80[EUR][1000 genomes]
rs4388466	0.80[EUR][1000 genomes]
rs4498545	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs4872957	0.81[EUR][1000 genomes]
rs4873102	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4873106	1.00[CEU][hapmap];0.87[CHD][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs4873293	0.97[EUR][1000 genomes]
rs4873437	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs6472229	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6981790	0.96[EUR][1000 genomes]
rs6982620	1.00[ASW][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap]
rs6990123	1.00[ASW][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6994218	0.94[EUR][1000 genomes]
rs7012341	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7819806	0.81[EUR][1000 genomes]
rs7826284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7839134	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs902619	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015347	chr8:47698082-48318579	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv539593	chr8:47698082-48318579	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv2758155	chr8:48188989-48321308	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2759610	chr8:48188989-48321308	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv1817304	chr8:48205314-48321308	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1034660	chr8:48265109-48411279	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1018457	chr8:48289643-48321308	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2172121	KIAA0146	cis	parietal	SCAN
rs2172121	MCM4	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48248800-48309600	Weak transcription	Thymus	Thymus
2	chr8:48262400-48309600	Weak transcription	Fetal Stomach	stomach
3	chr8:48263200-48297200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr8:48266600-48297200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr8:48266800-48297000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr8:48267000-48295400	Weak transcription	HSMM	muscle
7	chr8:48267800-48295000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:48278800-48309000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr8:48279000-48291800	Weak transcription	Esophagus	oesophagus
10	chr8:48279000-48299600	Weak transcription	Spleen	Spleen
11	chr8:48279000-48310200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr8:48280600-48311200	Weak transcription	Aorta	Aorta
13	chr8:48281600-48291600	Weak transcription	Fetal Thymus	thymus
14	chr8:48282200-48301200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr8:48282200-48311200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr8:48282200-48312200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr8:48282400-48300200	Weak transcription	Primary T cells from cord blood	blood
18	chr8:48282400-48321200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr8:48282800-48292800	Weak transcription	Psoas Muscle	Psoas
20	chr8:48282800-48299800	Weak transcription	Dnd41	blood
21	chr8:48283600-48297200	Weak transcription	Right Atrium	heart
22	chr8:48283800-48300200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr8:48284000-48291600	Weak transcription	Lung	lung
24	chr8:48284000-48300400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr8:48284200-48300200	Weak transcription	Primary B cells from cord blood	blood
26	chr8:48284200-48301000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr8:48284600-48296600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr8:48288400-48292600	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr8:48288600-48294400	Enhancers	Fetal Lung	lung
30	chr8:48288600-48296600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr8:48288600-48296800	Enhancers	Stomach Mucosa	stomach
32	chr8:48288800-48294400	Enhancers	Fetal Intestine Small	intestine
33	chr8:48289000-48294000	Weak transcription	Gastric	stomach
34	chr8:48289000-48295600	Weak transcription	Fetal Muscle Leg	muscle
35	chr8:48289200-48297200	Weak transcription	K562	blood
36	chr8:48289400-48294400	Enhancers	Fetal Intestine Large	intestine
37	chr8:48289600-48292000	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr8:48290000-48291800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr8:48290000-48291800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr8:48290000-48292200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr8:48290000-48293600	Enhancers	HMEC	breast
42	chr8:48290000-48293600	Enhancers	NHEK	skin
43	chr8:48290400-48291600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr8:48290400-48291600	Weak transcription	Colonic Mucosa	Colon
45	chr8:48290400-48292200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr8:48290400-48293800	Weak transcription	Small Intestine	intestine
47	chr8:48290400-48295600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr8:48290400-48297200	Weak transcription	Left Ventricle	heart
49	chr8:48290400-48299600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr8:48290400-48311400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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