Variant report

Variant	rs6427545
Chromosome Location	chr1:160770515-160770516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160769451..160770985-chr1:160774299..160776734,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10797085	0.82[EUR][1000 genomes]
rs10908806	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11265484	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11265485	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12072397	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12072399	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1333064	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2769587	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34002161	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766378	0.85[JPT][hapmap]
rs4656930	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4656931	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656934	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs480104	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs482921	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs489442	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs501026	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs501137	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs506263	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs508578	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs512197	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs520316	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs527253	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs527766	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs535241	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs536015	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs540224	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs546669	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs560681	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs575217	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs579589	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6427544	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6656939	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6685774	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6691072	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7541298	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7553107	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7555137	0.85[EUR][1000 genomes]
rs7555286	1.00[CEU][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs790624	0.94[EUR][1000 genomes];0.96[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6427545	CLK2	cis	parietal	SCAN
rs6427545	CASQ1	cis	parietal	SCAN
rs6427545	PPOX	cis	cerebellum	SCAN
rs6427545	LY9	Cis_1M	lymphoblastoid	RTeQTL
rs6427545	SMG5	cis	cerebellum	SCAN
rs6427545	SLAMF6	cis	cerebellum	SCAN
rs6427545	SNORA42	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160765400-160772200	Enhancers	Dnd41	blood
2	chr1:160766200-160771400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr1:160766800-160771400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr1:160768000-160771200	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
5	chr1:160768000-160771600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:160768400-160770800	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
7	chr1:160768600-160770600	Active TSS	Thymus	Thymus
8	chr1:160768600-160771000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
9	chr1:160768600-160774000	Genic enhancers	Primary B cells from peripheral blood	blood
10	chr1:160768800-160772600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:160769000-160771600	Weak transcription	Spleen	Spleen
12	chr1:160769200-160771800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:160769600-160771800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
14	chr1:160769800-160770600	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr1:160769800-160770600	Enhancers	Fetal Thymus	thymus
16	chr1:160770000-160770600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
17	chr1:160770000-160771200	Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr1:160770200-160770800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr1:160770200-160771000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:160770200-160771200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:160770400-160770800	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:160770400-160770800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:160770400-160770800	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr1:160770400-160771000	Enhancers	Primary hematopoietic stem cells	blood
25	chr1:160770400-160771000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:160770400-160771000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:160770400-160771000	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr1:160770400-160771000	Flanking Active TSS	GM12878-XiMat	blood
29	chr1:160770400-160771400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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