Variant report

Variant	rs6661505
Chromosome Location	chr1:59356826-59356827
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59244354..59252225-chr1:59338738..59357283,49	K562	blood:
2	chr1:59341509..59344296-chr1:59355857..59358402,2	MCF-7	breast:
3	chr1:59247150..59249652-chr1:59355694..59357549,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177606	Chromatin interaction
ENSG00000234807	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10493253	0.87[CEU][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10789072	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[ASN][1000 genomes]
rs11207319	0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11207321	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[ASN][1000 genomes]
rs11207322	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];0.96[ASN][1000 genomes]
rs11207323	0.87[CEU][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11207325	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11207326	0.87[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11207332	0.91[MEX][hapmap]
rs12117564	0.87[CEU][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12122077	0.91[CEU][hapmap];0.86[JPT][hapmap]
rs12142126	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12409909	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1536159	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17118379	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2057596	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2716105	0.83[JPT][hapmap]
rs3015311	0.81[CHD][hapmap]
rs41287666	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6587841	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6658104	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6664131	0.81[CEU][hapmap]
rs6677752	0.91[CEU][hapmap];0.91[MEX][hapmap]
rs6681632	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6697107	0.87[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7528731	0.91[CEU][hapmap];0.91[MEX][hapmap]

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	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6661505	OMA1	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59319800-59361400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:59348000-59360800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:59351000-59360800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:59351200-59359000	Weak transcription	Brain Substantia Nigra	brain
5	chr1:59351400-59359200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:59351800-59360800	Weak transcription	Fetal Heart	heart
7	chr1:59352000-59359000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:59352200-59358800	Weak transcription	Colonic Mucosa	Colon
9	chr1:59352200-59359000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:59352400-59360800	Weak transcription	Brain Angular Gyrus	brain
11	chr1:59352800-59358600	Weak transcription	Gastric	stomach
12	chr1:59352800-59360600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:59353400-59360000	Weak transcription	Colon Smooth Muscle	Colon
14	chr1:59353400-59360800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:59353600-59359000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:59353600-59359000	Weak transcription	Fetal Lung	lung
17	chr1:59353600-59361200	Weak transcription	Ovary	ovary
18	chr1:59353800-59358200	Weak transcription	Psoas Muscle	Psoas
19	chr1:59353800-59358600	Weak transcription	Adipose Nuclei	Adipose
20	chr1:59353800-59358600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:59353800-59358800	Weak transcription	Lung	lung
22	chr1:59353800-59358800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:59353800-59358800	Weak transcription	Spleen	Spleen
24	chr1:59353800-59359000	Weak transcription	Left Ventricle	heart
25	chr1:59353800-59359400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:59354400-59357600	Enhancers	Fetal Intestine Large	intestine
27	chr1:59354400-59357800	Enhancers	Fetal Intestine Small	intestine
28	chr1:59354600-59359000	Weak transcription	Right Atrium	heart
29	chr1:59354800-59357200	Weak transcription	NHLF	lung
30	chr1:59354800-59360800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:59355000-59358400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr1:59355000-59359000	Weak transcription	HSMM	muscle
33	chr1:59355000-59359000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr1:59355000-59360000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:59355000-59360800	Weak transcription	HSMMtube	muscle
36	chr1:59355200-59358600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:59355200-59359000	Weak transcription	Pancreas	Pancrea
38	chr1:59355200-59360800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:59355600-59358200	Weak transcription	HUVEC	blood vessel
40	chr1:59355800-59359000	Weak transcription	Fetal Thymus	thymus
41	chr1:59355800-59359000	Weak transcription	Right Ventricle	heart
42	chr1:59355800-59360800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:59355800-59361000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:59355800-59361400	Weak transcription	NH-A	brain
45	chr1:59356000-59357200	Enhancers	Stomach Mucosa	stomach
46	chr1:59356000-59360800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr1:59356000-59361200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:59356200-59358400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:59356200-59359200	Weak transcription	Small Intestine	intestine
50	chr1:59356200-59360800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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