Variant report

Variant	rs540217
Chromosome Location	chr1:160670816-160670817
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1090799	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12117784	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs481433	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs483158	0.86[AMR][1000 genomes]
rs498940	0.82[AFR][1000 genomes]
rs499980	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs500836	0.99[AFR][1000 genomes]
rs507260	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs530133	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535664	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569567	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59156523	0.91[ASN][1000 genomes]
rs7521591	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[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	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831714	chr1:160581168-160776809	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv437213	chr1:160652730-160681836	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160654200-160671000	Weak transcription	Small Intestine	intestine
2	chr1:160655200-160673600	Weak transcription	Spleen	Spleen
3	chr1:160656200-160672000	Weak transcription	Dnd41	blood
4	chr1:160660400-160671200	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:160660400-160671200	Weak transcription	Thymus	Thymus
6	chr1:160660400-160671600	Weak transcription	Primary B cells from cord blood	blood
7	chr1:160662000-160671000	Weak transcription	GM12878-XiMat	blood
8	chr1:160662000-160671200	Weak transcription	Fetal Thymus	thymus
9	chr1:160662200-160672000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:160662400-160672000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:160666000-160673800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:160667400-160672800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr1:160668200-160671400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr1:160668600-160673000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr1:160669200-160671000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr1:160669200-160671200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:160669200-160672200	Enhancers	Duodenum Mucosa	Duodenum
18	chr1:160669200-160673400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:160669200-160674400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:160669200-160674800	Genic enhancers	Primary T cells from cord blood	blood
21	chr1:160669200-160675800	Genic enhancers	Primary T cells fromperipheralblood	blood
22	chr1:160669400-160671400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:160669800-160672400	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:160669800-160673600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr1:160669800-160674200	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr1:160670000-160671600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:160670400-160671000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:160670400-160671200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:160670400-160676600	Genic enhancers	Primary B cells from peripheral blood	blood
30	chr1:160670800-160671600	Genic enhancers	Monocytes-CD14+_RO01746	blood

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