Variant report

Variant	rs6582575
Chromosome Location	chr12:46227650-46227651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46218751..46220862-chr12:46226687..46229341,3	MCF-7	breast:
2	chr12:46226998..46229066-chr12:46229113..46231060,2	MCF-7	breast:
3	chr12:46225560..46228108-chr12:46232102..46234612,2	K562	blood:

Variant related genes	Relation type
ENSG00000189079	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10161001	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10161062	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10161510	1.00[CHD][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10161536	0.91[ASW][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap]
rs10506264	0.93[YRI][hapmap]
rs10880858	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11183135	1.00[EUR][1000 genomes]
rs11183136	1.00[EUR][1000 genomes]
rs11183171	1.00[MEX][hapmap]
rs11183197	1.00[EUR][1000 genomes]
rs11183199	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11183202	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11183248	0.93[YRI][hapmap]
rs11574971	0.91[ASW][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap]
rs12296933	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12297214	0.83[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12301665	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12302862	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs12305110	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12307979	0.80[YRI][hapmap];0.81[AFR][1000 genomes]
rs12309988	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12316361	0.85[AMR][1000 genomes]
rs12316726	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12321106	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28583490	1.00[EUR][1000 genomes]
rs55916269	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56338250	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58253063	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59340060	1.00[EUR][1000 genomes]
rs7132585	1.00[EUR][1000 genomes]
rs7133123	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7296694	1.00[ASW][hapmap];1.00[CHD][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7303119	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7304785	0.82[AFR][1000 genomes]
rs7308856	1.00[CHD][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7308893	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7309921	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7315365	1.00[EUR][1000 genomes]
rs74081382	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs74081384	1.00[EUR][1000 genomes]
rs74081401	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74084208	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7953515	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7964495	1.00[CHD][hapmap];1.00[MEX][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs7965539	1.00[YRI][hapmap]
rs7971936	1.00[CHD][hapmap]
rs7972499	0.93[YRI][hapmap]
rs7972650	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs7973967	0.86[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7975170	1.00[CHD][hapmap];1.00[MEX][hapmap];0.80[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7975408	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832396	chr12:46155424-46310583	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46164600-46230000	Weak transcription	Thymus	Thymus
2	chr12:46177600-46243400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:46182600-46230600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:46183800-46243400	Weak transcription	Small Intestine	intestine
5	chr12:46184600-46231200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:46186000-46233400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:46186800-46243400	Weak transcription	HSMMtube	muscle
8	chr12:46194000-46228200	Weak transcription	Fetal Stomach	stomach
9	chr12:46196400-46243200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:46198000-46229600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:46200600-46244000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:46201800-46233200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:46202200-46233200	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:46202600-46233400	Weak transcription	Brain Substantia Nigra	brain
15	chr12:46202600-46243400	Weak transcription	Aorta	Aorta
16	chr12:46202800-46230400	Weak transcription	Left Ventricle	heart
17	chr12:46202800-46237800	Weak transcription	Lung	lung
18	chr12:46202800-46243200	Weak transcription	Ovary	ovary
19	chr12:46202800-46243200	Weak transcription	Right Ventricle	heart
20	chr12:46203800-46243800	Weak transcription	Spleen	Spleen
21	chr12:46204000-46230200	Weak transcription	Brain Anterior Caudate	brain
22	chr12:46204000-46233600	Weak transcription	Psoas Muscle	Psoas
23	chr12:46204200-46233200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr12:46205000-46230200	Weak transcription	Osteobl	bone
25	chr12:46207000-46230200	Weak transcription	HMEC	breast
26	chr12:46207400-46244400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:46208400-46228200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:46213200-46233200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr12:46213800-46228200	Strong transcription	Dnd41	blood
30	chr12:46214400-46244000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:46214600-46233600	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:46214800-46233600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:46215800-46230200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:46215800-46233000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:46215800-46244000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:46216200-46230200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:46216200-46233400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:46216200-46244000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr12:46216400-46233000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:46216400-46233000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:46217000-46230400	Weak transcription	Hela-S3	cervix
42	chr12:46217200-46231200	Weak transcription	NHEK	skin
43	chr12:46217800-46229800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:46218000-46230200	Weak transcription	HUVEC	blood vessel
45	chr12:46218000-46233200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:46218200-46230200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:46218200-46230200	Weak transcription	NH-A	brain
48	chr12:46218200-46230600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:46218200-46230600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr12:46218400-46230000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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