Variant report

Variant	rs9474680
Chromosome Location	chr6:53768929-53768930
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:53768489..53771106-chr6:53771711..53773800,2	MCF-7	breast:
2	chr6:53762030..53763793-chr6:53766610..53769238,2	K562	blood:
3	chr6:53762293..53765107-chr6:53765198..53769238,3	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10456168	0.81[EUR][1000 genomes]
rs10755768	0.87[EUR][1000 genomes]
rs12663216	0.81[JPT][hapmap]
rs2050159	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2820217	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs3003498	0.80[JPT][hapmap]
rs34299171	0.80[EUR][1000 genomes]
rs35081045	0.84[EUR][1000 genomes]
rs4265034	0.82[ASN][1000 genomes]
rs4478409	0.81[JPT][hapmap]
rs4486000	0.80[JPT][hapmap]
rs4582388	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4624872	0.90[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs4715428	0.84[EUR][1000 genomes]
rs4715429	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6458973	0.89[EUR][1000 genomes]
rs6906326	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6906921	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs6907027	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs6907354	0.89[EUR][1000 genomes]
rs6916929	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6925391	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6935942	0.81[EUR][1000 genomes]
rs7744962	0.80[EUR][1000 genomes]
rs7751036	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs9296722	0.82[ASN][1000 genomes]
rs9357777	0.86[EUR][1000 genomes]
rs9370245	0.87[EUR][1000 genomes]
rs9382254	0.86[CHB][hapmap]
rs9395884	0.80[ASN][1000 genomes]
rs9395887	0.82[ASN][1000 genomes]
rs9395890	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs9395891	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs9463988	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9463996	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.97[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9463997	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9474671	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53739000-53771800	Weak transcription	Pancreas	Pancrea
2	chr6:53752400-53771000	Weak transcription	Gastric	stomach
3	chr6:53752400-53771800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:53752800-53782000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:53754800-53775600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:53754800-53779800	Weak transcription	NHLF	lung
7	chr6:53755000-53779800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:53756000-53781800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:53758000-53775600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:53759200-53769400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:53759200-53770800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:53759200-53787600	Weak transcription	Spleen	Spleen
13	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
14	chr6:53759400-53770000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr6:53759400-53771800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:53759400-53786400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:53759600-53789800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:53760400-53789400	Weak transcription	Stomach Mucosa	stomach
19	chr6:53760400-53791200	Weak transcription	Hela-S3	cervix
20	chr6:53760600-53773000	Strong transcription	Dnd41	blood
21	chr6:53760600-53778800	Weak transcription	Fetal Muscle Leg	muscle
22	chr6:53760600-53793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr6:53760800-53771800	Weak transcription	Brain Angular Gyrus	brain
24	chr6:53761000-53770800	Weak transcription	Brain Substantia Nigra	brain
25	chr6:53761000-53771200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr6:53761000-53771600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:53761000-53771800	Weak transcription	Brain Anterior Caudate	brain
28	chr6:53761000-53782000	Weak transcription	Fetal Kidney	kidney
29	chr6:53761000-53782800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr6:53761000-53785400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr6:53761400-53771800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:53761400-53776400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr6:53761400-53787400	Weak transcription	HMEC	breast
34	chr6:53761400-53791200	Weak transcription	Colon Smooth Muscle	Colon
35	chr6:53761600-53771000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:53761600-53790800	Weak transcription	Fetal Heart	heart
37	chr6:53761800-53772400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr6:53761800-53777000	Strong transcription	Fetal Thymus	thymus
39	chr6:53761800-53786800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:53762000-53769200	Weak transcription	HSMM	muscle
41	chr6:53762000-53769800	Weak transcription	Osteobl	bone
42	chr6:53762000-53774000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr6:53762000-53775600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:53762000-53791200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:53762000-53791600	Weak transcription	Fetal Lung	lung
46	chr6:53762200-53786800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:53762800-53769400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:53762800-53775600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:53763000-53772200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:53763200-53769200	Weak transcription	Primary B cells from peripheral blood	blood

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