Variant report

Variant	rs9316396
Chromosome Location	chr13:49108010-49108011
allele	A/G
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	POLR2A	chr13:49105070-49108079	GM15510	blood:	n/a	n/a
2	POLR2A	chr13:49104184-49108569	GM19099	blood:	n/a	n/a
3	POLR2A	chr13:49105979-49108447	PBDE	blood:	n/a	n/a
4	POLR2A	chr13:49104358-49108010	GM18526	blood:	n/a	n/a
5	POLR2A	chr13:49104093-49108393	GM19193	blood:	n/a	n/a
6	MAZ	chr13:49106053-49108571	IMR90	lung:	n/a	chr13:49106870-49106879 chr13:49107330-49107340
7	POLR2A	chr13:49102123-49108646	GM12891	blood:	n/a	n/a
8	POLR2A	chr13:49104148-49108484	GM18505	blood:	n/a	n/a
9	POLR2A	chr13:49103707-49108625	GM12878	blood:	n/a	n/a
10	POLR2A	chr13:49107829-49108022	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr13:49104171-49108266	GM18951	blood:	n/a	n/a
12	STAT3	chr13:49107967-49108021	GM12878	blood:	n/a	n/a
13	POLR2A	chr13:49104669-49108203	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49107619..49110446-chr13:49111219..49113821,2	MCF-7	breast:

Variant related genes	Relation type
RCBTB2	TF binding region

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10076	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs12583514	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12583787	1.00[ASN][1000 genomes]
rs12585384	1.00[ASN][1000 genomes]
rs12857866	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1547660	0.83[AMR][1000 genomes]
rs17071695	1.00[CHD][hapmap]
rs17071937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174857	0.87[TSI][hapmap]
rs174858	1.00[CEU][hapmap];1.00[CHD][hapmap]
rs1926597	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs198571	0.87[TSI][hapmap]
rs198574	0.81[MEX][hapmap];0.87[TSI][hapmap]
rs198580	1.00[CEU][hapmap]
rs198582	1.00[CEU][hapmap]
rs198589	1.00[CEU][hapmap]
rs198606	0.87[TSI][hapmap]
rs198614	0.87[TSI][hapmap]
rs198617	1.00[CHD][hapmap]
rs198618	1.00[CHD][hapmap]
rs2148515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2156910	1.00[CEU][hapmap]
rs2804085	1.00[CHD][hapmap]
rs2897587	0.89[EUR][1000 genomes]
rs3020646	1.00[CHD][hapmap]
rs367438	1.00[CEU][hapmap]
rs3751380	0.85[TSI][hapmap]
rs406098	0.87[TSI][hapmap]
rs411862	1.00[CHD][hapmap]
rs4151463	1.00[CEU][hapmap]
rs4151469	1.00[CEU][hapmap]
rs4151475	1.00[CEU][hapmap]
rs4151479	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4151480	1.00[CEU][hapmap]
rs4151498	1.00[CEU][hapmap]
rs4151505	1.00[CEU][hapmap]
rs4151522	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4151524	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4151529	1.00[CEU][hapmap]
rs4151536	1.00[CEU][hapmap]
rs4151567	1.00[CEU][hapmap]
rs4151590	1.00[CHD][hapmap]
rs4151598	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4151602	1.00[ASN][1000 genomes]
rs4151610	1.00[CEU][hapmap]
rs4151613	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs449151	1.00[CEU][hapmap]
rs449268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs55686933	1.00[ASN][1000 genomes]
rs57394470	1.00[ASN][1000 genomes]
rs6561461	1.00[TSI][hapmap]
rs6650379	1.00[ASN][1000 genomes]
rs7139763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7319276	1.00[ASN][1000 genomes]
rs7325962	1.00[TSI][hapmap]
rs7326934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7332631	1.00[CHD][hapmap]
rs73479216	0.83[ASN][1000 genomes]
rs73479220	1.00[ASN][1000 genomes]
rs73495018	1.00[ASN][1000 genomes]
rs73495037	1.00[ASN][1000 genomes]
rs74074915	1.00[ASN][1000 genomes]
rs74074916	1.00[ASN][1000 genomes]
rs74074942	1.00[ASN][1000 genomes]
rs74074944	1.00[ASN][1000 genomes]
rs74074946	1.00[ASN][1000 genomes]
rs74074951	1.00[ASN][1000 genomes]
rs74077638	1.00[ASN][1000 genomes]
rs7992129	0.83[AMR][1000 genomes]
rs8001241	1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs8002565	0.83[AMR][1000 genomes]
rs9316384	1.00[ASN][1000 genomes]
rs9316386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316387	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9316392	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs9316398	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316401	0.83[AMR][1000 genomes]
rs9331984	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9331994	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9331999	1.00[CEU][hapmap]
rs9332025	1.00[CHD][hapmap]
rs9332031	1.00[CEU][hapmap]
rs9332033	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9332037	1.00[CEU][hapmap]
rs9332044	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9332049	1.00[CEU][hapmap]
rs9332053	1.00[GIH][hapmap]
rs9332055	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9332066	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs9332070	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9332085	1.00[ASN][1000 genomes]
rs9591171	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs9591176	1.00[ASN][1000 genomes]
rs9595894	1.00[CHD][hapmap]
rs9595914	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9595924	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9595926	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9595929	0.89[EUR][1000 genomes]

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	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49106200-49108400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr13:49107200-49108200	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr13:49107200-49108200	Flanking Active TSS	GM12878-XiMat	blood
4	chr13:49107200-49108600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
5	chr13:49107200-49110800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr13:49107400-49108200	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr13:49107400-49108200	Enhancers	Stomach Mucosa	stomach
8	chr13:49107400-49108400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr13:49107600-49108200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr13:49107600-49108200	Enhancers	Fetal Brain Male	brain
11	chr13:49107600-49108400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
12	chr13:49107600-49108400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr13:49107600-49108400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr13:49107600-49108400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr13:49107600-49108400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr13:49107600-49108600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr13:49107600-49108800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr13:49107800-49108200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:49107800-49108200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr13:49107800-49108200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr13:49107800-49108200	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr13:49107800-49108200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr13:49107800-49108200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr13:49107800-49108200	Enhancers	Fetal Stomach	stomach
25	chr13:49107800-49108400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr13:49107800-49108400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr13:49107800-49108400	Enhancers	Brain Anterior Caudate	brain
28	chr13:49107800-49108400	Enhancers	Brain Cingulate Gyrus	brain
29	chr13:49107800-49108400	Enhancers	Brain Hippocampus Middle	brain
30	chr13:49107800-49108400	Enhancers	Placenta	Placenta
31	chr13:49107800-49108600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr13:49107800-49108600	Enhancers	Primary T cells fromperipheralblood	blood
33	chr13:49107800-49108600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr13:49107800-49108600	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr13:49107800-49108600	Enhancers	Colon Smooth Muscle	Colon
36	chr13:49107800-49108600	Enhancers	Fetal Heart	heart
37	chr13:49107800-49108600	Enhancers	Dnd41	blood
38	chr13:49107800-49108800	Enhancers	Fetal Thymus	thymus
39	chr13:49107800-49110400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr13:49107800-49110400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr13:49107800-49110800	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr13:49107800-49116200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr13:49107800-49116200	Weak transcription	Left Ventricle	heart
44	chr13:49107800-49116200	Weak transcription	Right Atrium	heart
45	chr13:49107800-49116200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr13:49107800-49116400	Weak transcription	Lung	lung
47	chr13:49107800-49116800	Weak transcription	Pancreas	Pancrea
48	chr13:49108000-49108200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr13:49108000-49108200	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr13:49108000-49108200	Enhancers	HUES6 Cell Line	embryonic stem cell

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