Variant report

Variant	rs10947021
Chromosome Location	chr6:11205040-11205041
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:11204667..11206711-chr6:11213545..11215532,2	MCF-7	breast:
2	chr6:11201732..11205267-chr6:11223600..11226865,3	MCF-7	breast:
3	chr6:11204929..11207313-chr6:11318207..11320828,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf228-2	chr6:11204110-11205155	ENSG00000249190

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10484448	0.86[MEX][hapmap]
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]
rs10947026	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];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	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs12190858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200095	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12200932	0.86[MEX][hapmap]
rs12205037	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215094	0.89[CEU][hapmap];0.94[GIH][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs12215491	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17496632	1.00[JPT][hapmap]
rs2034	0.92[EUR][1000 genomes]
rs2327332	0.89[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3778169	1.00[CEU][hapmap];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	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs3798734	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs3798736	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3798737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798743	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs3823016	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6912916	0.95[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs6937575	0.89[CEU][hapmap];0.94[GIH][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs726230	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs729747	0.82[CEU][hapmap]
rs9295813	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];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:119 , 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	chr6:11199200-11205400	Weak transcription	Right Ventricle	heart
10	chr6:11199400-11212600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:11200400-11205600	Strong transcription	Primary B cells from peripheral blood	blood
12	chr6:11201000-11208600	Genic enhancers	Fetal Thymus	thymus
13	chr6:11201600-11206000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:11201600-11206000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:11201600-11206200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:11201600-11206600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr6:11201600-11207800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr6:11201600-11209600	Weak transcription	Fetal Brain Female	brain
19	chr6:11201600-11211000	Weak transcription	Gastric	stomach
20	chr6:11201800-11206600	Weak transcription	NHEK	skin
21	chr6:11201800-11213000	Weak transcription	Esophagus	oesophagus
22	chr6:11202400-11205200	Weak transcription	Colonic Mucosa	Colon
23	chr6:11202400-11205400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:11202400-11206600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:11202600-11206000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:11202600-11206000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:11202600-11207000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:11202800-11206000	Weak transcription	Dnd41	blood
29	chr6:11203000-11205200	Enhancers	Fetal Brain Male	brain
30	chr6:11203000-11207200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:11203000-11207200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr6:11203200-11206800	Strong transcription	HSMM	muscle
33	chr6:11203200-11207000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:11203200-11208000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:11203400-11205200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr6:11203400-11205600	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:11203400-11205600	Strong transcription	HSMMtube	muscle
38	chr6:11203400-11206200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:11203400-11206800	Weak transcription	Fetal Intestine Large	intestine
40	chr6:11203400-11209800	Weak transcription	Spleen	Spleen
41	chr6:11203600-11205200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:11203600-11205200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:11203600-11207000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr6:11203600-11208400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr6:11203800-11205200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr6:11203800-11205400	Enhancers	Brain Anterior Caudate	brain
47	chr6:11203800-11206400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:11203800-11206600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:11203800-11206600	Strong transcription	Osteobl	bone
50	chr6:11203800-11207400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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