Variant report

Variant	rs9468342
Chromosome Location	chr6:28298604-28298605
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28104111..28106206-chr6:28296771..28301344,4	K562	blood:
2	chr6:28103055..28111556-chr6:28296771..28308203,17	K562	blood:
3	chr6:28184981..28190782-chr6:28297491..28307222,23	K562	blood:
4	chr6:28265276..28267226-chr6:28297300..28300691,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198315	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000261839	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10456362	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1076639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755032	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11965538	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13200462	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1339899	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1419183	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1679709	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1679732	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16893735	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs1778507	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1778508	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1778511	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1936365	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs213239	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs213241	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs213243	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs213244	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2743554	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2743555	0.80[ASN][1000 genomes]
rs2799077	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2799079	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs3757188	1.00[YRI][hapmap]
rs68141011	0.81[ASN][1000 genomes]
rs6901575	1.00[JPT][hapmap]
rs6920512	1.00[CHB][hapmap];0.90[YRI][hapmap];0.87[ASN][1000 genomes]
rs73742521	0.94[EUR][1000 genomes]
rs853676	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs853678	0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs853679	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs853681	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs853682	0.87[ASN][1000 genomes]
rs853685	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs853687	0.91[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853688	0.91[ASN][1000 genomes]
rs853694	0.86[ASN][1000 genomes]
rs9295765	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap]
rs9366717	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs9380064	1.00[YRI][hapmap]
rs9393902	1.00[YRI][hapmap]
rs9393908	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs9461446	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9461448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9461449	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9468321	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9468322	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9468325	0.94[AFR][1000 genomes]
rs9468345	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9986596	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28288200-28299200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:28294800-28302000	Weak transcription	HepG2	liver
3	chr6:28294800-28302800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:28295400-28301400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:28295400-28302400	Weak transcription	Brain Angular Gyrus	brain
6	chr6:28295400-28302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr6:28295400-28303000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:28295400-28303000	Weak transcription	Thymus	Thymus
9	chr6:28295600-28302000	Weak transcription	Fetal Heart	heart
10	chr6:28295600-28302200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:28295600-28302200	Weak transcription	Hela-S3	cervix
12	chr6:28295600-28302400	Weak transcription	Brain Substantia Nigra	brain
13	chr6:28295600-28302600	Weak transcription	Stomach Mucosa	stomach
14	chr6:28295600-28302800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:28295600-28302800	Weak transcription	Fetal Brain Male	brain
16	chr6:28295800-28302800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:28297000-28302000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:28297000-28302800	Weak transcription	Colonic Mucosa	Colon
19	chr6:28297000-28303400	Weak transcription	Gastric	stomach
20	chr6:28297200-28300400	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:28297200-28302200	Weak transcription	Brain Anterior Caudate	brain
22	chr6:28297200-28302200	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:28297200-28302400	Weak transcription	Adipose Nuclei	Adipose
24	chr6:28297200-28302400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:28297200-28302400	Weak transcription	Pancreas	Pancrea
26	chr6:28297200-28302400	Weak transcription	Right Ventricle	heart
27	chr6:28297200-28302600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr6:28297200-28302800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:28297200-28302800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:28297200-28302800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:28297200-28302800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:28297200-28302800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:28297200-28303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:28297400-28301400	Weak transcription	Lung	lung
35	chr6:28297400-28301800	Weak transcription	Colon Smooth Muscle	Colon
36	chr6:28297400-28302200	Weak transcription	Fetal Brain Female	brain
37	chr6:28297400-28302400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr6:28297400-28302400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr6:28297400-28302400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:28297400-28302400	Weak transcription	Fetal Stomach	stomach
41	chr6:28297400-28302400	Weak transcription	Left Ventricle	heart
42	chr6:28297400-28302400	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr6:28297400-28302800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:28297400-28302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:28297400-28302800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:28297400-28302800	Weak transcription	Fetal Intestine Large	intestine
47	chr6:28297400-28302800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr6:28297400-28302800	Weak transcription	Psoas Muscle	Psoas
49	chr6:28297400-28303400	Weak transcription	Ovary	ovary
50	chr6:28297400-28303400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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