Variant report

Variant	rs897391
Chromosome Location	chr12:123326374-123326375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123325084..123327709-chr12:123347219..123349157,2	MCF-7	breast:
2	chr12:123311285..123313219-chr12:123325523..123328002,2	MCF-7	breast:
3	chr12:123255502..123257176-chr12:123324408..123327320,2	MCF-7	breast:
4	chr12:123324513..123326875-chr12:123435236..123437199,2	MCF-7	breast:
5	chr12:123324539..123327696-chr12:123450573..123452120,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150967	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10744422	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10744434	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10773599	0.81[YRI][hapmap]
rs10773627	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10773657	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10847742	0.81[YRI][hapmap]
rs10847749	0.81[YRI][hapmap]
rs10847751	0.81[YRI][hapmap]
rs10847775	0.80[YRI][hapmap]
rs10847826	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10847869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11060064	0.82[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs11060065	0.82[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs11060152	0.81[YRI][hapmap]
rs11060208	0.83[ASN][1000 genomes]
rs11060209	0.92[ASN][1000 genomes]
rs12255	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12298664	0.90[ASN][1000 genomes]
rs12299742	0.88[ASN][1000 genomes]
rs12313006	0.86[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs12314494	0.90[ASN][1000 genomes]
rs12314544	0.86[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12319654	0.90[ASN][1000 genomes]
rs12426809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532835	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1587856	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1671681	0.81[YRI][hapmap]
rs1671682	0.80[YRI][hapmap]
rs1671685	0.90[ASN][1000 genomes]
rs1696322	0.89[YRI][hapmap]
rs1696326	0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1696349	0.90[ASN][1000 genomes]
rs1798561	0.81[YRI][hapmap]
rs1798569	0.81[YRI][hapmap]
rs1799618	0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1979236	0.90[ASN][1000 genomes]
rs1979237	0.90[ASN][1000 genomes]
rs2061098	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2061101	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2100500	0.90[ASN][1000 genomes]
rs2135014	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271049	0.85[ASN][1000 genomes]
rs2271050	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs2271051	0.86[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap]
rs2292131	0.90[ASN][1000 genomes]
rs2292132	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292134	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292135	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292136	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2292138	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2343108	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2343109	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2343685	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2649908	0.89[ASN][1000 genomes]
rs2649909	0.90[ASN][1000 genomes]
rs2880678	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3817094	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3825143	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]
rs3844369	0.81[YRI][hapmap]
rs3852536	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3852537	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3896870	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4307760	0.81[YRI][hapmap]
rs4759355	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4759381	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4759382	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4759386	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4759387	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4759389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4759392	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4759393	0.81[ASW][hapmap];0.83[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap]
rs56272219	0.90[ASN][1000 genomes]
rs59922385	0.90[ASN][1000 genomes]
rs60308342	0.88[ASN][1000 genomes]
rs6489245	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap]
rs6489247	0.83[CEU][hapmap]
rs7138398	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7139055	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs7294991	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7303024	0.90[ASN][1000 genomes]
rs7309225	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73421642	0.90[ASN][1000 genomes]
rs735378	0.90[ASN][1000 genomes]
rs7398546	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs754080	0.90[ASN][1000 genomes]
rs7957643	0.81[CEU][hapmap];0.81[YRI][hapmap]
rs7959441	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7972447	0.94[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7980541	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs839360	0.86[CHB][hapmap]
rs897385	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs897386	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs897392	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs897393	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs921808	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs936083	0.83[CEU][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs937520	0.88[ASN][1000 genomes]
rs937766	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs967281	0.80[YRI][hapmap]

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	nsv560490	chr12:123326374-123346971	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs897391	HIP1R	cis	parietal	SCAN
rs897391	CCDC62	cis	cerebellum	SCAN
rs897391	ACADS	cis	parietal	SCAN
rs897391	VPS37B	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123321600-123326400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:123321600-123327200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:123321600-123332800	Weak transcription	Ovary	ovary
4	chr12:123321600-123333000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:123321800-123336800	Weak transcription	Aorta	Aorta
6	chr12:123322000-123332400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr12:123322400-123329000	Weak transcription	Thymus	Thymus
8	chr12:123322600-123332600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:123322800-123327200	Enhancers	Liver	Liver
10	chr12:123322800-123329600	Weak transcription	Spleen	Spleen
11	chr12:123322800-123334000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:123322800-123334400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:123322800-123339600	Weak transcription	Dnd41	blood
14	chr12:123322800-123353000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:123323000-123326600	Weak transcription	K562	blood
16	chr12:123323000-123330400	Genic enhancers	Primary B cells from peripheral blood	blood
17	chr12:123323200-123326800	Genic enhancers	NHEK	skin
18	chr12:123323200-123340800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr12:123323200-123352000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr12:123323400-123335200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:123323600-123326600	Strong transcription	Primary T cells from cord blood	blood
22	chr12:123323600-123332400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:123323600-123340800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr12:123323800-123326400	Genic enhancers	Duodenum Mucosa	Duodenum
25	chr12:123323800-123326600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:123323800-123327600	Genic enhancers	Fetal Intestine Small	intestine
27	chr12:123323800-123329200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:123323800-123331000	Enhancers	Stomach Mucosa	stomach
29	chr12:123324000-123327400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:123324200-123326800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr12:123324200-123327200	Strong transcription	Primary B cells from cord blood	blood
32	chr12:123324400-123326400	Enhancers	Right Ventricle	heart
33	chr12:123324400-123326600	Enhancers	NHLF	lung
34	chr12:123324400-123326800	Enhancers	Muscle Satellite Cultured Cells	--
35	chr12:123324400-123328200	Enhancers	Lung	lung
36	chr12:123324400-123328400	Enhancers	Placenta Amnion	Placenta Amnion
37	chr12:123324600-123326400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:123324600-123326600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:123324600-123326600	Enhancers	Psoas Muscle	Psoas
40	chr12:123324600-123326800	Enhancers	Esophagus	oesophagus
41	chr12:123324600-123326800	Enhancers	NHDF-Ad	bronchial
42	chr12:123324600-123327400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:123324600-123327600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:123324600-123330400	Enhancers	Right Atrium	heart
45	chr12:123324600-123330600	Enhancers	Left Ventricle	heart
46	chr12:123324600-123330800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:123324600-123344800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr12:123324600-123352800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr12:123324800-123326600	Enhancers	A549	lung
50	chr12:123324800-123327600	Enhancers	Skeletal Muscle Female	skeletal muscle

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