Variant report

Variant	rs502900
Chromosome Location	chr6:75999794-75999795
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	chr6:75993069..75997866-chr6:75997918..76002426,9	MCF-7	breast:
2	chr6:75993232..75997783-chr6:75998816..76002122,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225793	Chromatin interaction
ENSG00000112697	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1018471	0.90[GIH][hapmap]
rs10806035	0.82[GIH][hapmap]
rs10943241	0.83[CEU][hapmap]
rs13220419	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2207600	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2250989	0.90[GIH][hapmap]
rs240380	0.88[GIH][hapmap]
rs2703711	0.81[EUR][1000 genomes]
rs2703715	0.83[CEU][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs2748252	0.90[GIH][hapmap]
rs2748253	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808188	0.83[CEU][hapmap];0.81[CHB][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs2808201	0.81[CHB][hapmap]
rs2808208	0.81[EUR][1000 genomes]
rs2842451	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs2842455	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs2842461	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2951934	0.83[CEU][hapmap];0.81[CHB][hapmap];0.80[EUR][1000 genomes]
rs2951937	0.83[CEU][hapmap];0.81[CHB][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap]
rs2951939	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs2951945	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs2951946	0.81[EUR][1000 genomes]
rs2951947	0.81[EUR][1000 genomes]
rs2951952	0.83[CEU][hapmap];0.81[CHB][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes]
rs2998371	0.81[EUR][1000 genomes]
rs4295446	0.81[EUR][1000 genomes]
rs4324739	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs4380723	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs4541712	0.83[CEU][hapmap]
rs4568415	0.83[CEU][hapmap]
rs4706592	0.83[CEU][hapmap]
rs4708178	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4708179	0.82[GIH][hapmap]
rs4708181	0.83[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs6453825	0.82[CEU][hapmap];0.80[CHB][hapmap]
rs6913979	0.83[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs6921940	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs7451911	0.83[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs7753528	0.83[CEU][hapmap];0.81[CHB][hapmap]
rs7766441	0.83[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs7772989	0.83[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs9341514	0.83[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs9343281	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9352202	0.82[GIH][hapmap]
rs9352204	0.81[EUR][1000 genomes]
rs9352205	0.81[EUR][1000 genomes]
rs9443168	0.81[EUR][1000 genomes]
rs9443171	0.83[CEU][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs9689477	0.83[CEU][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription 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 miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	nsv603763	chr6:75923605-76009426	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv603764	chr6:75963751-76025603	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv830698	chr6:75968810-76115592	Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs502900	TMEM30A	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75995200-76010000	Weak transcription	Lung	lung
2	chr6:75995200-76016800	Weak transcription	Left Ventricle	heart
3	chr6:75995400-76021800	Weak transcription	Right Ventricle	heart
4	chr6:75995400-76027600	Weak transcription	Aorta	Aorta
5	chr6:75995600-75999800	Weak transcription	Brain Germinal Matrix	brain
6	chr6:75995600-76009600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:75995800-75999800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:75995800-75999800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:75995800-75999800	Weak transcription	Fetal Brain Male	brain
10	chr6:75995800-75999800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:75995800-76000000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:75995800-76000000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr6:75995800-76000200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:75995800-76000200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr6:75995800-76000400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr6:75995800-76000600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:75995800-76001200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:75995800-76002600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:75995800-76002800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:75995800-76009000	Weak transcription	Colon Smooth Muscle	Colon
21	chr6:75995800-76009600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:75995800-76009600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:75995800-76009600	Weak transcription	Fetal Muscle Leg	muscle
24	chr6:75995800-76009600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr6:75995800-76009800	Weak transcription	Fetal Heart	heart
26	chr6:75995800-76018200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:75995800-76027200	Weak transcription	Fetal Stomach	stomach
28	chr6:75996000-76002600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr6:75996000-76002800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:75996000-76003200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:75996000-76004000	Weak transcription	Esophagus	oesophagus
32	chr6:75996000-76009800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr6:75996000-76022600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:75996200-76009800	Weak transcription	Small Intestine	intestine
35	chr6:75996400-75999800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:75996400-76004000	Weak transcription	Primary T cells from cord blood	blood
37	chr6:75996400-76007400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr6:75996400-76009800	Weak transcription	Adipose Nuclei	Adipose
39	chr6:75997200-76000200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr6:75997600-76000000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr6:75997600-76001200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:75997600-76009600	Weak transcription	Liver	Liver
43	chr6:75997800-76002000	Weak transcription	Dnd41	blood
44	chr6:75997800-76009800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr6:75998200-76001600	Weak transcription	GM12878-XiMat	blood
46	chr6:75998400-76010000	Weak transcription	Placenta	Placenta
47	chr6:75998600-76000000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr6:75999200-76001400	Enhancers	Pancreas	Pancrea
49	chr6:75999400-75999800	Enhancers	Brain Anterior Caudate	brain
50	chr6:75999400-76001000	Enhancers	HUES6 Cell Line	embryonic stem cell

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