Variant report

Variant	rs12977917
Chromosome Location	chr19:19693299-19693300
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	chr19:19684439..19686704-chr19:19692465..19694414,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12611058	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12974028	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12981270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12982628	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12985142	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1476459	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33982830	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34096655	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34316070	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34316527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34324119	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34424437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35209041	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35437712	1.00[ASW][hapmap];0.91[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35553578	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35842591	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56083851	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62134460	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62137783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62137816	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62137820	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62137822	0.89[EUR][1000 genomes]
rs7247165	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs73004920	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs750216	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv518076	chr19:19692579-19715794	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12977917	LMO2	trans	lymphoblastoid	seeQTL
rs12977917	EDG4	cis	multi-tissue	Pritchard

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19671600-19701800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr19:19672000-19704800	Weak transcription	Brain Angular Gyrus	brain
3	chr19:19674200-19699800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr19:19676200-19701600	Weak transcription	GM12878-XiMat	blood
5	chr19:19681200-19701600	Weak transcription	NHLF	lung
6	chr19:19681400-19701600	Weak transcription	Fetal Lung	lung
7	chr19:19681600-19701600	Weak transcription	Esophagus	oesophagus
8	chr19:19681600-19703200	Weak transcription	Dnd41	blood
9	chr19:19682000-19702200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr19:19682600-19700600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:19686600-19700600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:19687000-19701600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:19688400-19699000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:19689800-19698800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:19689800-19700600	Weak transcription	Thymus	Thymus
16	chr19:19689800-19701800	Weak transcription	Fetal Brain Female	brain
17	chr19:19690200-19694000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:19690600-19693400	Enhancers	Stomach Mucosa	stomach
19	chr19:19690600-19693800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:19691000-19698600	Weak transcription	Brain Germinal Matrix	brain
21	chr19:19691200-19699600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr19:19691200-19700600	Weak transcription	Primary T cells from cord blood	blood
23	chr19:19691400-19699200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr19:19691400-19699400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr19:19692400-19693400	Enhancers	Colonic Mucosa	Colon
26	chr19:19692400-19693400	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr19:19692400-19693800	Enhancers	Primary T cells fromperipheralblood	blood
28	chr19:19692400-19693800	Enhancers	Fetal Muscle Trunk	muscle
29	chr19:19692600-19693400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr19:19692800-19693400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr19:19692800-19693400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:19692800-19693400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr19:19692800-19693800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:19692800-19693800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:19693000-19693400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:19693000-19693600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:19693000-19701600	Weak transcription	Fetal Stomach	stomach
38	chr19:19693200-19693400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:19693200-19693400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:19693200-19693400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:19693200-19693600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:19693200-19695200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr19:19693200-19701000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr19:19693200-19702200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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