Variant report

Variant	rs3825143
Chromosome Location	chr12:123352179-123352180
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123352169..123352839-chr12:123436532..123437356,4	MCF-7	breast:
2	chr12:123341988..123344732-chr12:123349863..123352592,2	MCF-7	breast:
3	chr12:123351930..123352762-chr12:123436973..123437518,2	MCF-7	breast:
4	chr12:123351397..123354786-chr12:123371825..123377880,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130787	Chromatin interaction
ENSG00000139722	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10744422	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10744434	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773627	0.94[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10773657	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10847826	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10847869	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11060064	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs11060065	0.81[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs12255	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12298151	0.90[ASN][1000 genomes]
rs12313006	0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs12314544	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs12426809	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1532835	0.92[EUR][1000 genomes]
rs1587856	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1696326	0.86[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs1799618	0.86[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs2061098	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2061101	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2135014	0.92[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs2271049	0.89[ASN][1000 genomes]
rs2271050	0.92[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs2271051	0.85[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.92[ASN][1000 genomes]
rs2292132	0.90[EUR][1000 genomes]
rs2292134	0.92[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes]
rs2292135	0.92[EUR][1000 genomes]
rs2292136	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2292138	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292139	0.92[ASN][1000 genomes]
rs2343108	0.91[EUR][1000 genomes]
rs2343109	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2343685	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2880678	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3817094	0.90[EUR][1000 genomes]
rs3852536	0.92[EUR][1000 genomes]
rs3852537	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4759355	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4759381	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4759382	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4759386	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4759387	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4759389	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4759392	0.81[AMR][1000 genomes]
rs4759393	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs59192320	0.92[ASN][1000 genomes]
rs6489245	0.94[ASW][hapmap];0.92[CEU][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs7138398	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7139055	0.92[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs7294991	0.81[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs7309225	0.92[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs7959441	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7972447	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7980541	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs839360	0.86[CHB][hapmap]
rs897385	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs897386	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs897391	0.94[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs897392	0.83[AMR][1000 genomes]
rs897393	0.94[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs921808	0.94[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs936083	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs937766	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv899574	chr12:123316566-123360151	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv899575	chr12:123326374-123360151	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3825143	HIP1R	cis	parietal	SCAN
rs3825143	ACADS	cis	parietal	SCAN
rs3825143	CCDC62	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123322800-123353000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:123324600-123352800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:123327400-123352600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr12:123327600-123353400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:123329200-123355000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:123332600-123355600	Strong transcription	Thymus	Thymus
7	chr12:123337400-123356200	Weak transcription	Fetal Kidney	kidney
8	chr12:123338800-123354200	Strong transcription	Brain Germinal Matrix	brain
9	chr12:123339000-123353200	Weak transcription	K562	blood
10	chr12:123339200-123354200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr12:123339600-123354200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:123339600-123355000	Strong transcription	Fetal Brain Female	brain
13	chr12:123341200-123352200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:123344400-123355000	Genic enhancers	Primary B cells from peripheral blood	blood
15	chr12:123344600-123353000	Enhancers	Liver	Liver
16	chr12:123344800-123355200	Weak transcription	Hela-S3	cervix
17	chr12:123345000-123353600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr12:123345200-123352600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr12:123345200-123354000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:123345200-123355400	Weak transcription	Fetal Brain Male	brain
21	chr12:123345400-123352200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:123345400-123353800	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:123345400-123354400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:123345600-123355400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:123345800-123352800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:123345800-123354000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:123346200-123352800	Weak transcription	Colon Smooth Muscle	Colon
28	chr12:123346400-123352400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:123347200-123354800	Strong transcription	Fetal Stomach	stomach
30	chr12:123347400-123355000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr12:123347600-123353800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr12:123347600-123354200	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr12:123347600-123355200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:123347800-123355000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:123348000-123352200	Strong transcription	Lung	lung
36	chr12:123348000-123352200	Weak transcription	Right Atrium	heart
37	chr12:123348200-123352400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:123348200-123352400	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:123348200-123352800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:123348200-123354000	Strong transcription	Primary hematopoietic stem cells	blood
41	chr12:123348200-123355000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:123348200-123355600	Strong transcription	NHLF	lung
43	chr12:123348400-123352200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:123348400-123352200	Strong transcription	Esophagus	oesophagus
45	chr12:123348400-123353000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:123348400-123354800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:123348600-123352400	Strong transcription	Duodenum Mucosa	Duodenum
48	chr12:123348800-123352200	Strong transcription	A549	lung
49	chr12:123348800-123354800	Strong transcription	Stomach Smooth Muscle	stomach
50	chr12:123348800-123355400	Strong transcription	NH-A	brain

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