Variant report

Variant	rs1879869
Chromosome Location	chr7:150345903-150345904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:150345053..150347622-chr7:150357976..150360904,2	MCF-7	breast:
2	chr7:150343613..150346226-chr7:150351593..150354204,2	K562	blood:
3	chr7:150341180..150342757-chr7:150345704..150347785,2	K562	blood:
4	chr7:150345226..150346892-chr7:150353382..150356343,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10155859	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224387	0.91[JPT][hapmap]
rs10225462	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10227548	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10228706	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10230559	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10235151	0.86[JPT][hapmap];0.82[TSI][hapmap]
rs10238979	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10243000	0.90[ASN][1000 genomes]
rs10243208	0.87[EUR][1000 genomes]
rs10243355	0.90[ASN][1000 genomes]
rs10252841	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253490	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10255380	0.87[EUR][1000 genomes]
rs10258838	0.88[EUR][1000 genomes]
rs10274439	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10275039	0.85[ASN][1000 genomes]
rs10275417	0.85[ASN][1000 genomes]
rs10278670	0.85[ASN][1000 genomes]
rs10282548	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1071922	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10952281	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11763374	0.88[EUR][1000 genomes]
rs11766040	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11768445	0.88[EUR][1000 genomes]
rs11770532	0.83[EUR][1000 genomes]
rs12111764	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1879868	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879870	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049248	0.91[ASN][1000 genomes]
rs2373817	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2373845	0.90[ASN][1000 genomes]
rs2373846	0.87[ASN][1000 genomes]
rs2373847	0.87[ASN][1000 genomes]
rs3088115	0.81[JPT][hapmap];0.82[TSI][hapmap]
rs3735085	0.81[JPT][hapmap];0.82[TSI][hapmap]
rs4490747	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4629771	0.89[ASN][1000 genomes]
rs4993563	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942976	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6944136	0.85[ASN][1000 genomes]
rs6947239	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6948827	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6952002	0.95[CEU][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs6969364	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6980253	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7357320	0.85[ASN][1000 genomes]
rs7808210	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	esv2758617	chr7:150251949-150463804	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2759573	chr7:150251949-150463804	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv3388935	chr7:150301204-150374532	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv831187	chr7:150325913-150503500	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1879869	MLL3	cis	parietal	SCAN
rs1879869	HCA112	cis	multi-tissue	Pritchard
rs1879869	GIMAP6	Cis_1M	lymphoblastoid	RTeQTL
rs1879869	LR8	cis	multi-tissue	Pritchard
rs1879869	GIMAP5	Cis_1M	lymphoblastoid	RTeQTL
rs1879869	TMEM176B	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150341800-150346800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr7:150341800-150347000	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr7:150341800-150347200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr7:150341800-150347200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:150341800-150347200	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr7:150342200-150346600	Enhancers	Primary T cells from cord blood	blood
7	chr7:150342800-150347400	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr7:150344000-150347000	Enhancers	Primary T cells fromperipheralblood	blood
9	chr7:150344000-150347000	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr7:150344400-150346600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr7:150344600-150346200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr7:150344800-150346800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr7:150344800-150347000	Enhancers	GM12878-XiMat	blood
14	chr7:150345000-150346400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr7:150345400-150346800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr7:150345800-150346200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:150345800-150346400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr7:150345800-150346400	Enhancers	Placenta	Placenta
19	chr7:150345800-150346600	Enhancers	Fetal Thymus	thymus
20	chr7:150345800-150346800	Enhancers	Dnd41	blood

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