Variant report

Variant	rs559290
Chromosome Location	chr6:33689956-33689957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33687230..33690069-chr6:34119183..34120791,2	MCF-7	breast:
2	chr6:33678022..33679887-chr6:33687741..33690570,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2229638	0.94[YRI][hapmap]
rs4711333	1.00[CHD][hapmap]
rs4713647	1.00[CHD][hapmap]
rs485623	1.00[CHD][hapmap]
rs523076	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs525623	1.00[CHD][hapmap];0.85[GIH][hapmap]
rs557559	1.00[CHD][hapmap]
rs560218	1.00[CHD][hapmap]
rs572708	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs62398913	0.93[EUR][1000 genomes]
rs637135	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs653536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs653825	0.85[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72880503	0.85[EUR][1000 genomes]
rs7757722	1.00[CHD][hapmap]
rs791900	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs942637	1.00[ASW][hapmap];0.90[MKK][hapmap];0.94[YRI][hapmap]

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:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33680000-33690000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:33680000-33690200	Weak transcription	Psoas Muscle	Psoas
3	chr6:33680000-33693000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:33680000-33695200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:33680000-33695800	Weak transcription	Spleen	Spleen
6	chr6:33680000-33696200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:33680000-33698400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:33680000-33705000	Weak transcription	Brain Angular Gyrus	brain
9	chr6:33685200-33693400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:33686200-33700200	Weak transcription	Liver	Liver
11	chr6:33686400-33691600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:33686400-33691800	Weak transcription	Colon Smooth Muscle	Colon
13	chr6:33686400-33710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:33686600-33690000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:33686600-33690600	Weak transcription	Right Ventricle	heart
16	chr6:33686600-33695800	Weak transcription	Right Atrium	heart
17	chr6:33686600-33698600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:33687400-33691200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:33687400-33692600	Enhancers	Stomach Mucosa	stomach
20	chr6:33687400-33694000	Weak transcription	Brain Anterior Caudate	brain
21	chr6:33687800-33693200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr6:33688000-33692000	Weak transcription	Brain Substantia Nigra	brain
23	chr6:33688200-33690200	Weak transcription	Fetal Lung	lung
24	chr6:33688600-33690000	Enhancers	Primary B cells from peripheral blood	blood
25	chr6:33688800-33690000	Weak transcription	Gastric	stomach
26	chr6:33688800-33698200	Weak transcription	Lung	lung
27	chr6:33688800-33700000	Strong transcription	HSMM	muscle
28	chr6:33689200-33696800	Strong transcription	HSMMtube	muscle
29	chr6:33689400-33695000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr6:33689600-33690600	Strong transcription	Placenta	Placenta
31	chr6:33689600-33690800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr6:33689600-33691000	Strong transcription	Brain Hippocampus Middle	brain
33	chr6:33689600-33691800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr6:33689600-33691800	Enhancers	Pancreas	Pancrea
35	chr6:33689600-33694600	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:33689600-33696600	Enhancers	Fetal Brain Male	brain
37	chr6:33689800-33691000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr6:33689800-33691800	Genic enhancers	Left Ventricle	heart

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