Variant report

Variant	rs546669
Chromosome Location	chr1:160768471-160768472
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160750574..160752770-chr1:160766750..160768788,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10797085	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10908806	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11265484	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11265485	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12072397	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12072399	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1333064	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2769587	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34002161	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4656930	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4656931	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4656934	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs482921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs489442	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs501026	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs501137	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs506263	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs508578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512197	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520316	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs527253	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs527766	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535241	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536015	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540224	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs560681	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs575217	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs579589	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6427544	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427545	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6656939	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6685774	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6691072	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7541298	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553107	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7555137	0.87[EUR][1000 genomes]
rs7555286	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs790624	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv464161	chr1:160747615-160852046	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv548057	chr1:160747615-160852046	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs546669	LY9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160765400-160772200	Enhancers	Dnd41	blood
2	chr1:160765800-160769200	Flanking Active TSS	Fetal Thymus	thymus
3	chr1:160766200-160771400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr1:160766800-160771400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr1:160767000-160768600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr1:160767000-160768800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:160767800-160768800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:160767800-160769400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:160768000-160768600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr1:160768000-160768600	Flanking Active TSS	Thymus	Thymus
11	chr1:160768000-160769600	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr1:160768000-160769800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr1:160768000-160769800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:160768000-160769800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr1:160768000-160770000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr1:160768000-160771200	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
17	chr1:160768000-160771600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:160768200-160768600	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
19	chr1:160768200-160768800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:160768200-160768800	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr1:160768200-160769000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:160768200-160770400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:160768200-160770400	Enhancers	Duodenum Mucosa	Duodenum
24	chr1:160768400-160769000	Enhancers	Spleen	Spleen
25	chr1:160768400-160769400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:160768400-160770400	Enhancers	GM12878-XiMat	blood
27	chr1:160768400-160770800	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood

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