Variant report

Variant	rs474131
Chromosome Location	chr1:160793442-160793443
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	chr1:160779738..160781417-chr1:160790589..160793548,2	K562	blood:
2	chr1:160791268..160793471-chr1:160795431..160798157,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLAMF7-9	chr1:160793298-160793586	NONHSAT007077
2	lnc-SLAMF7-9	chr1:160793256-160793586	NONHSAT007078

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11265487	0.87[ASN][1000 genomes]
rs11265488	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11265489	0.85[CEU][hapmap]
rs2027015	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2779800	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];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485618	0.92[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs492874	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs492906	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs494091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs496201	0.96[ASN][1000 genomes]
rs504848	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs505728	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs506081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs509749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510143	0.97[ASN][1000 genomes]
rs512645	0.92[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs516509	0.99[ASN][1000 genomes]
rs516847	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs522897	0.97[ASN][1000 genomes]
rs539433	0.97[ASN][1000 genomes]
rs551827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551882	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs556810	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs567306	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs569659	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs569911	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs571841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs574610	0.89[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576334	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs577453	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427548	0.88[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6667581	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs790625	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs790626	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	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
4	nsv825087	chr1:160793152-160793980	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
5	nsv825098	chr1:160793398-160793980	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
6	nsv825109	chr1:160793398-160794018	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
7	nsv825120	chr1:160793398-160794045	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
8	nsv825131	chr1:160793398-160794075	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
9	nsv825143	chr1:160793409-160794018	Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs474131	CLK2	cis	parietal	SCAN
rs474131	DEDD	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160771000-160806600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:160778000-160795600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:160778000-160798400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr1:160778400-160799600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:160782400-160798200	Strong transcription	Primary T helper cells PMA-I stimulated	--
6	chr1:160782600-160803200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:160783800-160798200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:160783800-160801000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:160783800-160803200	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr1:160790000-160794200	Strong transcription	Primary B cells from cord blood	blood
11	chr1:160790600-160803000	Strong transcription	Primary T cells from cord blood	blood
12	chr1:160791000-160794400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:160791200-160795000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:160791200-160798200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr1:160791200-160800000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:160792000-160794000	Strong transcription	Thymus	Thymus
17	chr1:160792400-160794400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
18	chr1:160792400-160794400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:160792400-160798600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr1:160792600-160794400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:160792800-160794000	Strong transcription	Spleen	Spleen
22	chr1:160792800-160794200	Strong transcription	Fetal Thymus	thymus
23	chr1:160793000-160811600	Weak transcription	Gastric	stomach
24	chr1:160793200-160794400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:160793400-160807400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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