Variant report

Variant	rs9403564
Chromosome Location	chr6:144858217-144858218
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144848573..144853071-chr6:144854031..144858388,6	K562	blood:
2	chr6:144854161..144860088-chr6:144861624..144865343,8	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12661566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12663647	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12664494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12664819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1534442	0.80[JPT][hapmap]
rs1534443	0.80[JPT][hapmap]
rs17073972	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs17073995	1.00[MEX][hapmap]
rs1918751	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1918752	0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1997252	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2056744	0.92[MEX][hapmap]
rs2091486	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2293536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3811100	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4076068	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4896728	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs6906465	0.80[JPT][hapmap]
rs9321980	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9373415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap]
rs9376823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9376824	1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs9376826	0.89[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9376828	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9386070	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9386071	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9386072	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9386073	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9390170	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390172	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9390174	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9390175	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9390176	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9390178	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9399480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9399481	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9403563	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs9403567	0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9497009	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[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	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1015228	chr6:144780458-144989321	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv538462	chr6:144780458-144989321	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr6:144803400-144869800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:144807400-144904000	Weak transcription	Brain Substantia Nigra	brain
3	chr6:144812400-144881000	Weak transcription	Stomach Mucosa	stomach
4	chr6:144812600-144869800	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:144815200-144881000	Weak transcription	NHEK	skin
6	chr6:144816600-144881400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:144821200-144861000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:144829800-144863800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:144831400-144879000	Strong transcription	Primary B cells from cord blood	blood
10	chr6:144832400-144862200	Weak transcription	Small Intestine	intestine
11	chr6:144833800-144868200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr6:144837200-144880800	Weak transcription	Brain Angular Gyrus	brain
13	chr6:144844400-144861400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr6:144844400-144870000	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:144844600-144860800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:144850000-144864200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:144850000-144864200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:144850200-144858600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:144850200-144877400	Weak transcription	HMEC	breast
20	chr6:144850400-144864000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr6:144850400-144864200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:144850400-144865600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:144850400-144866000	Weak transcription	Hela-S3	cervix
24	chr6:144850400-144903200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:144850400-144903200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:144850400-144904200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:144850600-144862200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:144850600-144863400	Weak transcription	Fetal Intestine Small	intestine
29	chr6:144850600-144863600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:144850600-144865800	Weak transcription	NHLF	lung
31	chr6:144850600-144870800	Weak transcription	Right Ventricle	heart
32	chr6:144850600-144881600	Weak transcription	Brain Anterior Caudate	brain
33	chr6:144850800-144861000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr6:144850800-144863600	Weak transcription	Colonic Mucosa	Colon
35	chr6:144851600-144861600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:144852200-144862000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr6:144852400-144861000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:144852400-144861000	Weak transcription	Esophagus	oesophagus
39	chr6:144852400-144861000	Weak transcription	Thymus	Thymus
40	chr6:144852400-144861400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:144852400-144862000	Weak transcription	Spleen	Spleen
42	chr6:144852400-144870600	Weak transcription	Aorta	Aorta
43	chr6:144852600-144860000	Weak transcription	Placenta	Placenta
44	chr6:144852600-144860400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr6:144852800-144859200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr6:144852800-144860400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:144853000-144861600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr6:144853600-144863400	Weak transcription	Lung	lung
49	chr6:144853600-144896400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr6:144853800-144863600	Weak transcription	Fetal Stomach	stomach

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