Variant report

Variant	rs12205398
Chromosome Location	chr6:33701543-33701544
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33700010..33701892-chr6:33765256..33768196,2	MCF-7	breast:
2	chr6:33701443..33703598-chr6:33706736..33709323,2	K562	blood:
3	chr6:33700581..33702116-chr6:33711630..33713944,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10456075	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10456420	0.87[AFR][1000 genomes]
rs10947426	0.87[AFR][1000 genomes]
rs10947432	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12153870	0.87[AFR][1000 genomes]
rs12189725	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12190155	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12192035	0.85[ASN][1000 genomes]
rs12193658	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12195409	0.87[AFR][1000 genomes]
rs12195707	0.87[AFR][1000 genomes]
rs12199132	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12203688	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204620	0.87[AFR][1000 genomes]
rs12204992	0.87[AFR][1000 genomes]
rs12205667	0.87[AFR][1000 genomes]
rs12211490	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12211554	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12211565	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12215329	0.88[ASN][1000 genomes]
rs12660955	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12661400	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12662447	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13200063	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13204162	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204975	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13206228	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13207666	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13213889	0.83[ASN][1000 genomes]
rs13214874	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13220421	0.87[AFR][1000 genomes]
rs2274459	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2281831	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281917	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2281918	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2281919	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2296737	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2296749	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs34139049	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34339105	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34460651	0.87[AFR][1000 genomes]
rs34472165	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34517899	0.87[AFR][1000 genomes]
rs34778247	0.91[EUR][1000 genomes]
rs34869648	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34884883	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35088242	0.87[AFR][1000 genomes]
rs35095444	0.83[EUR][1000 genomes]
rs35274562	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35445446	0.87[AFR][1000 genomes]
rs35646598	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35698850	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35721478	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs35797388	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs36097803	0.87[AFR][1000 genomes]
rs36122085	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3818526	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3818532	0.94[EUR][1000 genomes]
rs66670017	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs68168863	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs729376	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs751095	0.88[ASN][1000 genomes]
rs755239	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs877187	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296097	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9469554	0.83[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	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33680000-33705000	Weak transcription	Brain Angular Gyrus	brain
2	chr6:33686400-33710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:33690800-33708200	Weak transcription	Gastric	stomach
4	chr6:33691800-33711600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:33692000-33706800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:33692000-33710200	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:33693600-33712000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:33694000-33710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:33695000-33702400	Weak transcription	Brain Anterior Caudate	brain
10	chr6:33695600-33711800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:33698200-33701600	Genic enhancers	Left Ventricle	heart
12	chr6:33698200-33702400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:33698400-33703000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr6:33698400-33703400	Strong transcription	Spleen	Spleen
15	chr6:33699200-33710000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:33699400-33703600	Genic enhancers	Right Ventricle	heart
17	chr6:33699800-33708000	Weak transcription	Fetal Lung	lung
18	chr6:33700000-33701600	Genic enhancers	Placenta	Placenta
19	chr6:33700000-33701600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
20	chr6:33700000-33705000	Weak transcription	Pancreas	Pancrea
21	chr6:33700200-33706600	Weak transcription	Fetal Intestine Large	intestine
22	chr6:33700400-33701600	Genic enhancers	Muscle Satellite Cultured Cells	--
23	chr6:33700400-33701600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr6:33700400-33707400	Weak transcription	Lung	lung
25	chr6:33700600-33701600	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
26	chr6:33700600-33703800	Strong transcription	HSMMtube	muscle
27	chr6:33700600-33704600	Weak transcription	Right Atrium	heart
28	chr6:33700600-33705200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:33700600-33707200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:33700800-33701600	Genic enhancers	Fetal Muscle Trunk	muscle
31	chr6:33700800-33701600	Genic enhancers	Fetal Muscle Leg	muscle
32	chr6:33700800-33703600	Strong transcription	Brain Substantia Nigra	brain
33	chr6:33700800-33703800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:33701000-33701600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:33701000-33701600	Enhancers	Fetal Brain Female	brain
36	chr6:33701000-33702200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:33701000-33705400	Weak transcription	Liver	Liver
38	chr6:33701200-33703400	Strong transcription	Brain Hippocampus Middle	brain
39	chr6:33701200-33704800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:33701400-33701600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:33701400-33701600	Bivalent Enhancer	Fetal Stomach	stomach
42	chr6:33701400-33702000	Strong transcription	HSMM	muscle
43	chr6:33701400-33702400	Weak transcription	Psoas Muscle	Psoas
44	chr6:33701400-33702600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr6:33701400-33703000	Weak transcription	HepG2	liver
46	chr6:33701400-33705000	Weak transcription	Brain Inferior Temporal Lobe	brain

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