Variant report

Variant	rs20499
Chromosome Location	chr6:13295004-13295005
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	chr6:13294633-13295075	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13276714..13280149-chr6:13292500..13295672,4	K562	blood:

Variant related genes	Relation type
ENSG00000272379	TF binding region
ENSG00000112137	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1223397	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs1223399	0.82[EUR][1000 genomes]
rs1223400	0.80[EUR][1000 genomes]
rs1223401	0.82[EUR][1000 genomes]
rs1223402	0.82[EUR][1000 genomes]
rs1223403	0.83[EUR][1000 genomes]
rs1232392	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13191897	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13205692	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17700321	1.00[CEU][hapmap];0.89[GIH][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs17767967	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs202016	0.82[ASN][1000 genomes]
rs202017	0.82[ASN][1000 genomes]
rs202018	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs202019	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs202021	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs202023	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2048552	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs20500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2439534	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2439535	0.82[ASN][1000 genomes]
rs2439537	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2439539	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2439540	0.81[ASN][1000 genomes]
rs2439541	0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2439542	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2439543	0.81[ASN][1000 genomes]
rs2439545	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2439548	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2439549	0.82[ASN][1000 genomes]
rs2458309	0.82[ASN][1000 genomes]
rs2458310	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2458311	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2458312	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2458314	0.81[JPT][hapmap]
rs2496140	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2496142	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2496144	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2496145	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2496147	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2496148	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2496149	0.82[ASN][1000 genomes]
rs2496151	0.82[ASN][1000 genomes]
rs2496152	0.82[ASN][1000 genomes]
rs2496153	0.82[ASN][1000 genomes]
rs2496154	0.82[ASN][1000 genomes]
rs2496156	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2496157	0.81[JPT][hapmap]
rs2919685	0.82[ASN][1000 genomes]
rs2919686	0.82[ASN][1000 genomes]
rs3001966	0.82[ASN][1000 genomes]
rs3001967	0.82[ASN][1000 genomes]
rs34505804	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35511719	0.91[EUR][1000 genomes]
rs35549743	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3734878	1.00[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3817737	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3817738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3817741	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3817742	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs402705	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs449727	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs452309	0.82[ASN][1000 genomes]
rs453877	0.91[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs617580	0.88[JPT][hapmap]
rs641758	0.81[JPT][hapmap]
rs9349564	0.82[ASN][1000 genomes]
rs9381884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9395602	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs957175	0.82[ASN][1000 genomes]
rs957176	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs20499	TBC1D7	cis	cerebellum	SCAN
rs20499	CD83	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
2	chr6:13285400-13302400	Weak transcription	HUVEC	blood vessel
3	chr6:13287000-13303600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:13287800-13295200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:13287800-13298200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:13288000-13296200	Strong transcription	Primary B cells from peripheral blood	blood
7	chr6:13288200-13295400	Weak transcription	Fetal Heart	heart
8	chr6:13288200-13296400	Strong transcription	GM12878-XiMat	blood
9	chr6:13288400-13302600	Weak transcription	Hela-S3	cervix
10	chr6:13288400-13302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:13288600-13296400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:13288600-13302400	Strong transcription	Fetal Brain Female	brain
13	chr6:13288600-13302600	Strong transcription	Fetal Muscle Leg	muscle
14	chr6:13288600-13321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:13288600-13326400	Strong transcription	Primary T cells from cord blood	blood
16	chr6:13289000-13295800	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr6:13289000-13299800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:13289800-13327000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:13290200-13302800	Weak transcription	NHEK	skin
20	chr6:13290400-13296200	Strong transcription	Fetal Thymus	thymus
21	chr6:13290400-13296800	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr6:13290400-13310400	Strong transcription	Dnd41	blood
23	chr6:13290600-13295600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:13290600-13296800	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr6:13290600-13302800	Weak transcription	Stomach Mucosa	stomach
26	chr6:13290800-13296400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:13291000-13295800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:13291000-13297200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:13291000-13297400	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr6:13291000-13302800	Strong transcription	Fetal Stomach	stomach
31	chr6:13291200-13303000	Strong transcription	Fetal Intestine Small	intestine
32	chr6:13291200-13310400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr6:13291400-13296400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:13291400-13297800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr6:13291400-13299600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr6:13291400-13300200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:13291400-13303600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:13291600-13295600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:13291600-13295600	Strong transcription	Brain Anterior Caudate	brain
40	chr6:13291600-13295600	Strong transcription	HSMMtube	muscle
41	chr6:13291600-13295800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:13291600-13295800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:13291600-13295800	Strong transcription	Adipose Nuclei	Adipose
44	chr6:13291600-13295800	Strong transcription	Brain Cingulate Gyrus	brain
45	chr6:13291600-13295800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:13291600-13296200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:13291600-13296200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:13291600-13296200	Strong transcription	Liver	Liver
49	chr6:13291600-13296200	Strong transcription	Brain Germinal Matrix	brain
50	chr6:13291600-13296400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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