Variant report

Variant	rs1059140
Chromosome Location	chr1:220324189-220324190
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:220322576..220325762-chr1:220328423..220332016,4	K562	blood:
2	chr1:220321298..220324435-chr1:220324859..220327837,3	K562	blood:
3	chr1:220168435..220171336-chr1:220322060..220324695,2	K562	blood:
4	chr1:220321221..220324929-chr1:220326199..220329423,4	MCF-7	breast:
5	chr1:220323753..220325549-chr2:43453479..43455067,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152518	Chromatin interaction
ENSG00000118873	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11547779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12032345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2289189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2289191	0.92[AMR][1000 genomes]
rs2292418	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2577165	1.00[JPT][hapmap]
rs3767655	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41274790	0.88[AMR][1000 genomes]
rs41274794	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs41303055	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1059140	RAB3GAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220268400-220330200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:220269400-220330000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:220284600-220324600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:220288200-220324600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:220296000-220327600	Weak transcription	Colonic Mucosa	Colon
6	chr1:220298800-220334600	Strong transcription	Fetal Thymus	thymus
7	chr1:220303800-220331600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:220304800-220335600	Strong transcription	Placenta	Placenta
9	chr1:220305400-220331800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:220305400-220347000	Strong transcription	Dnd41	blood
11	chr1:220305400-220376600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:220305600-220347600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:220305800-220347000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr1:220306600-220336600	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:220306600-220346600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:220306600-220348200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:220308400-220324800	Weak transcription	HSMMtube	muscle
18	chr1:220308400-220327600	Weak transcription	Aorta	Aorta
19	chr1:220308400-220329600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:220308400-220339600	Weak transcription	Psoas Muscle	Psoas
21	chr1:220310000-220324400	Strong transcription	Osteobl	bone
22	chr1:220310600-220327600	Weak transcription	Spleen	Spleen
23	chr1:220311200-220325000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:220311200-220330600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:220311200-220343400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:220311400-220330200	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:220311400-220331000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:220311600-220335000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr1:220312000-220331200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:220312200-220347400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:220313000-220327600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:220313200-220324600	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:220313200-220328600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:220314800-220325600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:220315000-220324800	Weak transcription	Brain Substantia Nigra	brain
36	chr1:220315200-220324600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:220315200-220324800	Weak transcription	Gastric	stomach
38	chr1:220315200-220327400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr1:220315200-220327600	Weak transcription	Right Ventricle	heart
40	chr1:220315400-220324600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:220315400-220324600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr1:220315400-220324600	Weak transcription	NHEK	skin
43	chr1:220315400-220325800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:220315400-220326600	Weak transcription	Fetal Brain Male	brain
45	chr1:220315400-220327600	Weak transcription	Brain Angular Gyrus	brain
46	chr1:220315600-220324800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr1:220315800-220324400	Weak transcription	Colon Smooth Muscle	Colon
48	chr1:220315800-220324600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:220315800-220325400	Weak transcription	Lung	lung
50	chr1:220315800-220325800	Weak transcription	Stomach Smooth Muscle	stomach

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