Variant report

Variant	rs512645
Chromosome Location	chr1:160798126-160798127
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	chr1:160791268..160793471-chr1:160795431..160798157,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11265487	0.84[ASN][1000 genomes]
rs11265488	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2027015	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2779800	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]
rs474131	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]
rs485618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs492874	0.96[ASN][1000 genomes]
rs492906	0.96[ASN][1000 genomes]
rs494091	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs496201	0.92[ASN][1000 genomes]
rs504848	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs505728	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs506081	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs509749	0.92[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs510143	0.93[ASN][1000 genomes]
rs516509	0.96[ASN][1000 genomes]
rs516847	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs522897	0.94[ASN][1000 genomes]
rs539433	0.94[ASN][1000 genomes]
rs551827	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs551882	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs556810	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs567306	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs569659	0.85[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs569911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571841	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs574610	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577453	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427548	0.81[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6667581	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs790625	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs790626	0.85[EUR][1000 genomes];0.97[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs512645	CLK2	cis	parietal	SCAN
rs512645	LY9	Cis_1M	lymphoblastoid	RTeQTL
rs512645	DEDD	cis	cerebellum	SCAN

Chromatin state (count:29 , 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	chr1:160778000-160798400	Strong transcription	Primary B cells from peripheral blood	blood
3	chr1:160778400-160799600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:160782400-160798200	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr1:160782600-160803200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:160783800-160798200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr1:160783800-160801000	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:160783800-160803200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr1:160790600-160803000	Strong transcription	Primary T cells from cord blood	blood
10	chr1:160791200-160798200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:160791200-160800000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:160792400-160798600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr1:160793000-160811600	Weak transcription	Gastric	stomach
14	chr1:160793400-160807400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:160794000-160805800	Weak transcription	Thymus	Thymus
16	chr1:160794000-160806200	Weak transcription	Spleen	Spleen
17	chr1:160794200-160803000	Weak transcription	Fetal Thymus	thymus
18	chr1:160795800-160798200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:160796200-160798200	Strong transcription	Primary B cells from cord blood	blood
20	chr1:160796400-160798200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:160796400-160800200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:160796600-160799000	Weak transcription	Primary hematopoietic stem cells	blood
23	chr1:160796800-160804800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:160797200-160798200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:160797200-160805000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:160797600-160805000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:160797600-160805200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:160797800-160799800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:160797800-160805600	Strong transcription	Monocytes-CD14+_RO01746	blood

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