Variant report

Variant	rs2038863
Chromosome Location	chr1:59402586-59402587
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:59390430..59392531-chr1:59402170..59404785,2	K562	blood:
2	chr1:59244790..59246539-chr1:59401387..59403438,2	K562	blood:
3	chr1:59244501..59246539-chr1:59401938..59403701,2	K562	blood:
4	chr1:59401291..59404305-chr1:59406315..59409384,3	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10158831	0.82[EUR][1000 genomes]
rs10789072	0.84[JPT][hapmap]
rs10889121	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11207331	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12090072	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12122077	0.80[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs1536159	0.80[JPT][hapmap]
rs2477745	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2716105	0.95[JPT][hapmap]
rs2716107	0.90[JPT][hapmap]
rs2716113	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2716115	0.88[CEU][hapmap];0.80[JPT][hapmap];0.88[EUR][1000 genomes]
rs2716127	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2764911	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2764914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2764915	0.87[CEU][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs2764917	0.88[CEU][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs2953376	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015311	0.90[JPT][hapmap]
rs3015312	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4528141	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4912382	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6677752	0.81[ASN][1000 genomes]
rs7528731	0.81[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

No data

Chromatin state (count:19 , 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	chr1:59398800-59403000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:59399000-59405800	Weak transcription	Pancreas	Pancrea
5	chr1:59399000-59406800	Weak transcription	Esophagus	oesophagus
6	chr1:59399000-59407000	Weak transcription	Lung	lung
7	chr1:59399200-59407200	Weak transcription	Colonic Mucosa	Colon
8	chr1:59399200-59409400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:59399400-59405200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:59399400-59405800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:59399600-59402800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:59399800-59402600	Weak transcription	HMEC	breast
13	chr1:59400600-59402800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:59400800-59402600	Weak transcription	NHEK	skin
15	chr1:59401600-59407000	Weak transcription	Gastric	stomach
16	chr1:59402000-59404000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr1:59402000-59404000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr1:59402200-59403400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:59402400-59402600	Enhancers	A549	lung

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