Variant report

Variant	rs9295665
Chromosome Location	chr6:25594379-25594380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:3776604..3777354-chr6:25594056..25594579,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000101224	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1022492	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10434845	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs12663643	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12665641	0.91[CHB][hapmap];0.93[YRI][hapmap]
rs13192159	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13201652	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs13203202	0.82[JPT][hapmap]
rs13217586	0.88[CEU][hapmap]
rs1406924	0.82[AMR][1000 genomes]
rs2049967	0.87[CEU][hapmap]
rs2072845	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2072848	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2072849	0.93[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2205935	0.82[JPT][hapmap]
rs2272824	0.93[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2328879	0.82[JPT][hapmap]
rs3747526	0.93[CEU][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3788992	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3804120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804122	0.81[ASN][1000 genomes]
rs3804123	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs3804124	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3804125	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3804126	0.93[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3804127	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3827505	0.93[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4588684	0.85[AMR][1000 genomes]
rs6935799	0.93[CEU][hapmap];0.86[CHB][hapmap];0.94[YRI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6939153	0.82[JPT][hapmap]
rs7738571	0.93[CEU][hapmap];0.95[CHB][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7739227	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7741329	0.92[CEU][hapmap]
rs7767930	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7776417	0.93[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9348683	0.93[CEU][hapmap];0.91[CHB][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9356979	0.86[CHB][hapmap];0.89[YRI][hapmap]
rs9356980	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9356981	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9356983	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9358860	0.80[ASN][1000 genomes]
rs9366625	0.86[CHB][hapmap];0.89[YRI][hapmap]
rs9379772	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9379776	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs9379777	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs9393648	0.91[CHB][hapmap]
rs9393649	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9393650	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941428	0.82[EUR][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	nsv883488	chr6:25592489-25731691	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25471600-25597200	Weak transcription	Gastric	stomach
2	chr6:25516800-25606400	Weak transcription	Lung	lung
3	chr6:25541600-25612000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:25547200-25600600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:25556200-25618000	Weak transcription	Primary B cells from cord blood	blood
6	chr6:25572000-25622200	Weak transcription	HSMMtube	muscle
7	chr6:25577200-25603400	Weak transcription	Fetal Brain Female	brain
8	chr6:25577200-25624800	Weak transcription	Adipose Nuclei	Adipose
9	chr6:25577600-25597200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:25579200-25604600	Weak transcription	Fetal Brain Male	brain
11	chr6:25580200-25597800	Weak transcription	Hela-S3	cervix
12	chr6:25580200-25599000	Weak transcription	NHEK	skin
13	chr6:25580600-25608600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:25580600-25610200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr6:25580800-25599600	Weak transcription	Small Intestine	intestine
16	chr6:25581200-25622800	Weak transcription	Colonic Mucosa	Colon
17	chr6:25582000-25594400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:25582000-25611400	Weak transcription	Brain Anterior Caudate	brain
19	chr6:25582000-25626800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr6:25582400-25622200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:25582800-25594400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:25583200-25600600	Weak transcription	Placenta	Placenta
23	chr6:25583600-25598600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:25583600-25623200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:25583800-25623200	Weak transcription	Esophagus	oesophagus
26	chr6:25584400-25597400	Weak transcription	NHDF-Ad	bronchial
27	chr6:25585000-25627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:25585200-25599600	Weak transcription	Fetal Kidney	kidney
29	chr6:25585200-25629400	Weak transcription	Pancreas	Pancrea
30	chr6:25587400-25622400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:25587600-25599200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:25587800-25598200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:25588000-25596200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr6:25589000-25603000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:25589000-25604600	Weak transcription	Fetal Thymus	thymus
36	chr6:25589200-25623400	Weak transcription	HMEC	breast
37	chr6:25590800-25618000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr6:25591000-25601600	Strong transcription	Primary T cells from cord blood	blood
39	chr6:25591200-25595800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:25591400-25594400	Strong transcription	Fetal Intestine Small	intestine
41	chr6:25591400-25595600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:25591400-25596200	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr6:25591600-25594600	Strong transcription	Aorta	Aorta
44	chr6:25592000-25594800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:25592000-25595600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:25592200-25594400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:25592400-25602400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:25592400-25625600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:25592600-25595200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:25592800-25594600	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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