Variant report

Variant	rs12190858
Chromosome Location	chr6:11206113-11206114
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:11201485..11204415-chr6:11205595..11207344,2	MCF-7	breast:
2	chr6:11204667..11206711-chr6:11213545..11215532,2	MCF-7	breast:
3	chr6:11197493..11200396-chr6:11205565..11209405,4	MCF-7	breast:
4	chr6:11204929..11207313-chr6:11318207..11320828,2	MCF-7	breast:
5	chr6:11205282..11206878-chr6:11230200..11231972,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10807059	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947017	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947020	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947026	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947036	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10947037	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12190771	0.83[EUR][1000 genomes]
rs12200095	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12205037	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215094	0.89[EUR][1000 genomes]
rs12215491	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2034	0.92[EUR][1000 genomes]
rs2327332	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3102	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734405	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3756966	0.92[EUR][1000 genomes]
rs3778169	0.92[EUR][1000 genomes]
rs3778170	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778171	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798733	0.92[EUR][1000 genomes]
rs3798734	0.92[EUR][1000 genomes]
rs3798736	0.92[EUR][1000 genomes]
rs3798737	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798738	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798743	0.89[EUR][1000 genomes]
rs3823016	1.00[ASN][1000 genomes]
rs6912916	0.90[EUR][1000 genomes]
rs6937575	0.89[EUR][1000 genomes]
rs726230	0.89[EUR][1000 genomes]
rs9295813	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS 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 target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11192800-11207000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr6:11192800-11207200	Weak transcription	Liver	Liver
3	chr6:11195400-11207200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:11195600-11207400	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:11197000-11211000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:11197000-11211200	Genic enhancers	HepG2	liver
7	chr6:11198200-11207000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr6:11198400-11206600	Genic enhancers	A549	lung
9	chr6:11199400-11212600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:11201000-11208600	Genic enhancers	Fetal Thymus	thymus
11	chr6:11201600-11206200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:11201600-11206600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr6:11201600-11207800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr6:11201600-11209600	Weak transcription	Fetal Brain Female	brain
15	chr6:11201600-11211000	Weak transcription	Gastric	stomach
16	chr6:11201800-11206600	Weak transcription	NHEK	skin
17	chr6:11201800-11213000	Weak transcription	Esophagus	oesophagus
18	chr6:11202400-11206600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:11202600-11207000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr6:11203000-11207200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:11203000-11207200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr6:11203200-11206800	Strong transcription	HSMM	muscle
23	chr6:11203200-11207000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:11203200-11208000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:11203400-11206200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:11203400-11206800	Weak transcription	Fetal Intestine Large	intestine
27	chr6:11203400-11209800	Weak transcription	Spleen	Spleen
28	chr6:11203600-11207000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:11203600-11208400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:11203800-11206400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:11203800-11206600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:11203800-11206600	Strong transcription	Osteobl	bone
33	chr6:11203800-11207400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr6:11203800-11207400	Weak transcription	Psoas Muscle	Psoas
35	chr6:11203800-11207600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr6:11203800-11209000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:11203800-11210200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr6:11203800-11213200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:11203800-11213400	Weak transcription	Brain Germinal Matrix	brain
40	chr6:11204000-11206600	Weak transcription	HMEC	breast
41	chr6:11204000-11206800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr6:11204000-11206800	Weak transcription	NHDF-Ad	bronchial
43	chr6:11204000-11207800	Weak transcription	Small Intestine	intestine
44	chr6:11204000-11208600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr6:11204000-11208600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr6:11204000-11208800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr6:11204000-11209600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:11204000-11209800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:11204000-11210600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:11204000-11211000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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