Variant report

Variant	rs897386
Chromosome Location	chr12:123341289-123341290
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123341219-123341478	K562	blood:	n/a	n/a
2	POLR2A	chr12:123341245-123341295	K562	blood:	n/a	n/a
3	POLR2A	chr12:123341098-123341441	H1-neurons	neurons:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123341218..123343418-chr12:123435392..123437282,2	MCF-7	breast:
2	chr12:123329734..123338030-chr12:123339120..123345153,11	MCF-7	breast:
3	chr12:123330610..123333935-chr12:123339820..123343037,3	MCF-7	breast:
4	chr11:65265725..65268508-chr12:123341267..123343973,2	MCF-7	breast:
5	chr12:123340470..123342158-chr12:123459989..123462897,2	K562	blood:
6	chr12:123319098..123320683-chr12:123341200..123343169,2	MCF-7	breast:

No data

Variant related genes	Relation type
HIP1R	TF binding region
ENSG00000111325	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000150967	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000251562	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10744422	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10744434	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10773599	0.81[CEU][hapmap]
rs10773627	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10773657	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10847742	0.81[CEU][hapmap]
rs10847749	0.81[CEU][hapmap]
rs10847751	0.82[CEU][hapmap]
rs10847775	0.82[YRI][hapmap]
rs10847826	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10847869	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11060064	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs11060065	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs11060152	0.81[CEU][hapmap]
rs12255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12298151	0.93[ASN][1000 genomes]
rs12298664	0.80[ASN][1000 genomes]
rs12299742	0.80[ASN][1000 genomes]
rs12313006	0.89[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs12314494	0.80[ASN][1000 genomes]
rs12314544	0.90[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs12319654	0.80[ASN][1000 genomes]
rs12369846	0.81[ASN][1000 genomes]
rs12426809	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1260121	0.81[CEU][hapmap]
rs1532835	0.93[EUR][1000 genomes]
rs1587856	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1671685	0.80[ASN][1000 genomes]
rs1671687	0.81[CEU][hapmap]
rs1696322	0.86[YRI][hapmap]
rs1696326	0.89[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs1696349	0.80[ASN][1000 genomes]
rs1798563	0.81[CEU][hapmap]
rs1799618	0.89[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs1975761	0.81[CEU][hapmap]
rs1979236	0.80[ASN][1000 genomes]
rs1979237	0.80[ASN][1000 genomes]
rs2061098	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2061101	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2100500	0.80[ASN][1000 genomes]
rs2135014	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes]
rs2271049	0.91[ASN][1000 genomes]
rs2271050	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2271051	0.89[CHB][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]
rs2292131	0.80[ASN][1000 genomes]
rs2292132	0.91[EUR][1000 genomes]
rs2292134	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2292135	0.93[EUR][1000 genomes]
rs2292136	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2292138	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292139	0.93[ASN][1000 genomes]
rs2343108	0.92[EUR][1000 genomes]
rs2343109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2343685	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2649895	0.81[CEU][hapmap]
rs2649896	0.81[CEU][hapmap]
rs2649903	0.82[CEU][hapmap]
rs2649909	0.80[ASN][1000 genomes]
rs2656812	0.81[CEU][hapmap]
rs2880678	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3817094	0.91[EUR][1000 genomes]
rs3825143	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]
rs3844369	0.81[CEU][hapmap]
rs3852536	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3852537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4307760	0.82[CEU][hapmap]
rs4759355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4759381	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4759382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4759386	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4759387	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4759389	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4759392	0.81[AMR][1000 genomes]
rs4759393	0.81[CEU][hapmap];0.89[CHB][hapmap]
rs56272219	0.80[ASN][1000 genomes]
rs59192320	0.94[ASN][1000 genomes]
rs59922385	0.80[ASN][1000 genomes]
rs6489241	0.82[CEU][hapmap]
rs6489245	1.00[CEU][hapmap]
rs6489247	0.81[CEU][hapmap]
rs7138398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7139055	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7294991	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes]
rs7303024	0.80[ASN][1000 genomes]
rs7309225	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs73421642	0.80[ASN][1000 genomes]
rs735378	0.80[ASN][1000 genomes]
rs7398546	0.83[AFR][1000 genomes]
rs754080	0.80[ASN][1000 genomes]
rs7957643	0.90[CEU][hapmap]
rs7959441	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7972447	1.00[CEU][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7980541	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs839354	0.81[CEU][hapmap]
rs839360	0.90[CHB][hapmap]
rs897385	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897391	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	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs897393	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs921808	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];0.92[EUR][1000 genomes]
rs936083	0.82[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs937520	0.80[ASN][1000 genomes]
rs937766	0.93[EUR][1000 genomes]
rs967281	0.81[CEU][hapmap]
rs9795629	0.81[CEU][hapmap]

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	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
9	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

No data

Chromatin state (count:112 , 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	chr12:123323200-123352000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:123324600-123344800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:123324600-123352800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:123324800-123351600	Weak transcription	Small Intestine	intestine
6	chr12:123326600-123345000	Weak transcription	A549	lung
7	chr12:123327200-123344200	Weak transcription	Hela-S3	cervix
8	chr12:123327400-123352600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:123327600-123353400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:123329200-123355000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:123329400-123341800	Weak transcription	HepG2	liver
12	chr12:123329600-123344600	Strong transcription	Fetal Intestine Small	intestine
13	chr12:123330400-123344400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr12:123330400-123349200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:123332200-123343200	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:123332600-123344800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr12:123332600-123355600	Strong transcription	Thymus	Thymus
18	chr12:123333000-123344400	Strong transcription	Spleen	Spleen
19	chr12:123333000-123344600	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr12:123333000-123345000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:123333800-123342800	Weak transcription	Ovary	ovary
22	chr12:123334400-123344400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:123335200-123347000	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:123335600-123342600	Strong transcription	Primary T cells from cord blood	blood
25	chr12:123336000-123342400	Genic enhancers	Brain Inferior Temporal Lobe	brain
26	chr12:123337200-123343400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:123337200-123348800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:123337400-123348400	Weak transcription	HSMM	muscle
29	chr12:123337400-123356200	Weak transcription	Fetal Kidney	kidney
30	chr12:123337600-123341800	Weak transcription	Fetal Lung	lung
31	chr12:123337600-123344200	Weak transcription	Placenta	Placenta
32	chr12:123337600-123344800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr12:123337600-123348200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:123337600-123351000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:123337600-123351400	Weak transcription	HSMMtube	muscle
36	chr12:123337800-123341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:123337800-123341800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:123337800-123342600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr12:123337800-123344800	Strong transcription	NHEK	skin
40	chr12:123337800-123346800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:123337800-123347600	Weak transcription	NH-A	brain
42	chr12:123337800-123351600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:123338000-123341800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:123338000-123342000	Genic enhancers	Brain Substantia Nigra	brain
45	chr12:123338200-123343000	Strong transcription	Liver	Liver
46	chr12:123338400-123342400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:123338400-123344600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:123338400-123344800	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:123338400-123344800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:123338400-123345200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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