Variant report

Variant	rs17096884
Chromosome Location	chr12:46770767-46770768
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr12:46770434-46770777	K562	blood:	n/a	n/a
2	TBL1XR1	chr12:46770538-46770796	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:46769817..46771459-chr12:46823347..46825693,2	K562	blood:
2	chr12:46769477..46772174-chr12:46953105..46955870,2	K562	blood:

Variant related genes	Relation type
SLC38A2	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10467215	0.82[CHB][hapmap]
rs10506267	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs10506268	1.00[EUR][1000 genomes]
rs11183454	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11183467	0.93[ASW][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes]
rs11183482	0.93[ASW][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes]
rs11183487	1.00[AMR][1000 genomes]
rs11183500	0.82[CHB][hapmap]
rs11183510	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs1125908	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11830769	1.00[EUR][1000 genomes]
rs11834593	0.85[ASN][1000 genomes]
rs11834905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12299499	0.84[CHB][hapmap];1.00[AMR][1000 genomes]
rs12317255	0.88[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes]
rs12320438	1.00[AMR][1000 genomes]
rs12321512	0.94[CHB][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap]
rs12321642	1.00[AMR][1000 genomes]
rs12321960	0.82[CHB][hapmap]
rs12322378	1.00[AMR][1000 genomes]
rs13377959	0.93[ASW][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes]
rs17096896	0.94[CHB][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes]
rs17096922	0.88[CHB][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes]
rs1948425	0.89[JPT][hapmap]
rs2125646	0.94[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes]
rs2307059	0.89[JPT][hapmap]
rs2307062	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2307063	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2408509	0.94[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34280632	1.00[AMR][1000 genomes]
rs35875247	1.00[AMR][1000 genomes]
rs36010856	1.00[AMR][1000 genomes]
rs3742061	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935048	0.89[CHD][hapmap]
rs4768118	0.81[YRI][hapmap]
rs55795804	0.81[ASN][1000 genomes]
rs56036156	1.00[AMR][1000 genomes]
rs56196954	1.00[AMR][1000 genomes]
rs56222195	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56314009	1.00[AMR][1000 genomes]
rs57067899	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57149475	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57271454	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57425661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58460251	1.00[AMR][1000 genomes]
rs58890669	1.00[AMR][1000 genomes]
rs59608605	1.00[AMR][1000 genomes]
rs60565802	1.00[AMR][1000 genomes]
rs60628240	1.00[EUR][1000 genomes]
rs60878594	1.00[AMR][1000 genomes]
rs60977966	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61232019	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61406609	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61517444	1.00[EUR][1000 genomes]
rs73282532	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73282561	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73282591	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73290315	1.00[AMR][1000 genomes]
rs74082254	1.00[AMR][1000 genomes]
rs74083707	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74083710	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74084031	1.00[EUR][1000 genomes]
rs7488027	1.00[AMR][1000 genomes]
rs7953339	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs7954314	0.93[ASW][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes]
rs7965618	1.00[AMR][1000 genomes]
rs7967889	0.88[CHB][hapmap];0.83[JPT][hapmap];1.00[AMR][1000 genomes]
rs7977319	1.00[AMR][1000 genomes]
rs7980023	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs923788	0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9669404	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46767800-46771200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:46767800-46771400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:46767800-46773800	Weak transcription	Pancreas	Pancrea
4	chr12:46767800-46774000	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:46767800-46774600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:46767800-46776200	Weak transcription	Small Intestine	intestine
7	chr12:46768000-46771400	Weak transcription	GM12878-XiMat	blood
8	chr12:46768000-46775600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr12:46768000-46776200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:46768000-46776200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:46768000-46776200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:46768000-46776200	Weak transcription	Brain Substantia Nigra	brain
13	chr12:46768000-46776200	Weak transcription	Placenta	Placenta
14	chr12:46768000-46776200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:46768000-46776400	Weak transcription	Gastric	stomach
16	chr12:46768000-46776400	Weak transcription	Left Ventricle	heart
17	chr12:46768000-46776400	Weak transcription	Psoas Muscle	Psoas
18	chr12:46768200-46771400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:46768200-46773800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:46768200-46775800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:46768200-46776000	Weak transcription	NH-A	brain
22	chr12:46768400-46771000	Enhancers	Liver	Liver
23	chr12:46768400-46771200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:46768400-46771200	Weak transcription	NHDF-Ad	bronchial
25	chr12:46768400-46771200	Weak transcription	Osteobl	bone
26	chr12:46768400-46773600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:46768400-46775600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:46768400-46775800	Weak transcription	A549	lung
29	chr12:46768400-46776000	Weak transcription	NHEK	skin
30	chr12:46768400-46776200	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr12:46768400-46776200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr12:46768400-46776400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:46768600-46775800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:46768600-46776200	Weak transcription	Thymus	Thymus
35	chr12:46768800-46770800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:46768800-46771400	Weak transcription	K562	blood
37	chr12:46768800-46771600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:46768800-46772200	Enhancers	HepG2	liver
39	chr12:46768800-46772800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:46768800-46772800	Enhancers	Hela-S3	cervix
41	chr12:46768800-46773800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:46768800-46774000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr12:46768800-46775600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:46768800-46775600	Weak transcription	NHLF	lung
45	chr12:46768800-46776000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr12:46768800-46776200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr12:46768800-46776200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr12:46769200-46772400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:46769200-46774000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:46769200-46776000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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