Variant report

Variant	rs240398
Chromosome Location	chr6:75980419-75980420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:75979886..75981407-chr6:75985729..75987544,2	K562	blood:
2	chr6:75979010..75981926-chr6:75992579..75994330,2	MCF-7	breast:
3	chr6:75979468..75981742-chr6:75992719..75994647,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112697	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs117512	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203213	0.89[EUR][1000 genomes]
rs147523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15616	0.87[EUR][1000 genomes]
rs240361	1.00[JPT][hapmap]
rs240367	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs240368	0.91[EUR][1000 genomes]
rs240369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs240381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240382	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240383	0.85[EUR][1000 genomes]
rs240385	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240388	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs240389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240390	0.85[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs240392	0.87[EUR][1000 genomes]
rs240393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240400	0.87[EUR][1000 genomes]
rs240401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240404	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs240405	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240409	0.94[EUR][1000 genomes]
rs240410	0.84[EUR][1000 genomes]
rs240419	0.82[AMR][1000 genomes]
rs240423	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs240428	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs240429	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240430	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240431	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240432	0.85[CEU][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs381141	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397039	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414624	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs418485	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs448854	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs507912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs542717	0.91[EUR][1000 genomes]
rs638590	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643707	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs654428	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9293996	1.00[MEX][hapmap]
rs9443152	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv463155	chr6:75789526-75980419	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv603762	chr6:75789526-75980419	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
8	nsv603763	chr6:75923605-76009426	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv603764	chr6:75963751-76025603	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS 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	14 gene(s)	inside rSNPs	diseases
10	nsv830698	chr6:75968810-76115592	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75953800-75982200	Weak transcription	Spleen	Spleen
2	chr6:75954400-75986000	Weak transcription	Brain Germinal Matrix	brain
3	chr6:75954600-75982400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr6:75954800-75982200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:75954800-75988200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:75960600-75981400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:75967800-75988200	Weak transcription	Fetal Brain Male	brain
8	chr6:75968600-75981600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:75969400-75981400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr6:75969600-75983800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:75969600-75992200	Weak transcription	Colonic Mucosa	Colon
12	chr6:75970000-75992400	Weak transcription	Brain Substantia Nigra	brain
13	chr6:75970200-75982000	Weak transcription	Brain Hippocampus Middle	brain
14	chr6:75973000-75985200	Weak transcription	HepG2	liver
15	chr6:75973200-75982200	Weak transcription	Thymus	Thymus
16	chr6:75973200-75985000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:75973400-75985600	Weak transcription	Lung	lung
18	chr6:75973400-75988200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:75973800-75982200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:75974000-75981600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr6:75974000-75982000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr6:75974000-75982200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr6:75974000-75986200	Weak transcription	K562	blood
24	chr6:75974000-75988000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr6:75974200-75981400	Weak transcription	Adipose Nuclei	Adipose
26	chr6:75974200-75982400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:75974200-75993000	Weak transcription	Placenta	Placenta
28	chr6:75974400-75981600	Weak transcription	Fetal Thymus	thymus
29	chr6:75974800-75981600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:75974800-75982000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr6:75974800-75989800	Weak transcription	Fetal Brain Female	brain
32	chr6:75975000-75981400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr6:75975000-75988200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr6:75975000-75992400	Weak transcription	Fetal Stomach	stomach
35	chr6:75975400-75981600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr6:75975400-75982000	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr6:75975600-75981200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr6:75975600-75982000	Weak transcription	Fetal Intestine Large	intestine
39	chr6:75975600-75982200	Weak transcription	Primary T cells from cord blood	blood
40	chr6:75975600-75982200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr6:75975800-75981800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr6:75976000-75982400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:75977200-75981400	Weak transcription	Fetal Lung	lung
44	chr6:75977400-75981800	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr6:75977400-75982000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:75977600-75981400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:75977600-75981600	Weak transcription	Colon Smooth Muscle	Colon
48	chr6:75977800-75981600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr6:75978200-75982000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:75978200-75982400	Weak transcription	Brain Anterior Caudate	brain

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