Variant report

Variant	rs6677752
Chromosome Location	chr1:59406024-59406025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59405293..59407465-chr1:59409123..59412417,3	K562	blood:
2	chr1:59249675..59251848-chr1:59404372..59406665,2	K562	blood:
3	chr1:59389648..59391930-chr1:59403285..59406048,2	K562	blood:
4	chr1:59246952..59251848-chr1:59405165..59409884,6	K562	blood:
5	chr1:59403568..59405263-chr1:59405379..59408693,3	K562	blood:

Variant related genes	Relation type
ENSG00000177606	Chromatin interaction
ENSG00000234807	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11207323	0.91[MEX][hapmap]
rs11207325	0.91[CEU][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes]
rs11207332	0.87[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12117564	0.91[MEX][hapmap]
rs12122077	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12404569	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1536159	0.91[CEU][hapmap]
rs2038863	0.81[ASN][1000 genomes]
rs2057596	0.83[CEU][hapmap]
rs2716127	0.88[ASN][1000 genomes]
rs2764914	0.81[CHB][hapmap]
rs2953373	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3015312	0.81[CHB][hapmap]
rs4912382	0.85[CHB][hapmap]
rs6658104	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs6661505	0.91[CEU][hapmap];0.91[MEX][hapmap]
rs6664131	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs74078024	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7528731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	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
3	nsv546316	chr1:59368947-59457815	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6677752	OMA1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59389000-59407000	Weak transcription	Spleen	Spleen
2	chr1:59393600-59406800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:59399000-59406800	Weak transcription	Esophagus	oesophagus
4	chr1:59399000-59407000	Weak transcription	Lung	lung
5	chr1:59399200-59407200	Weak transcription	Colonic Mucosa	Colon
6	chr1:59399200-59409400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:59401600-59407000	Weak transcription	Gastric	stomach
8	chr1:59402600-59408400	Weak transcription	A549	lung
9	chr1:59403200-59408000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:59403200-59408200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:59403200-59408200	Weak transcription	NHEK	skin
12	chr1:59403400-59408000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:59403400-59408200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:59403400-59408200	Weak transcription	HMEC	breast
15	chr1:59404400-59407200	Enhancers	Primary T cells fromperipheralblood	blood
16	chr1:59405000-59407200	Enhancers	Primary T cells from cord blood	blood
17	chr1:59405000-59407200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:59405200-59406200	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr1:59405200-59407000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:59405200-59407200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:59405200-59407200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr1:59405400-59410800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:59405600-59407000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr1:59405600-59407000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr1:59405600-59407000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr1:59405600-59407200	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr1:59405800-59406600	Weak transcription	Primary B cells from peripheral blood	blood
28	chr1:59405800-59407000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:59405800-59407200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:59406000-59407000	Weak transcription	Pancreas	Pancrea

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