Variant report

Variant	rs3099942
Chromosome Location	chr2:39098358-39098359
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39097841..39100728-chr2:39103293..39104847,2	MCF-7	breast:
2	chr2:39089505..39093700-chr2:39094409..39098372,5	K562	blood:
3	chr2:39095857..39098722-chr2:39101020..39103452,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163214	Chromatin interaction
ENSG00000188010	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1010858	0.88[EUR][1000 genomes]
rs1010859	0.85[GIH][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10204999	0.81[EUR][1000 genomes]
rs11124654	0.81[EUR][1000 genomes]
rs1131752	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11689954	0.82[EUR][1000 genomes]
rs12621073	0.88[EUR][1000 genomes]
rs12712625	0.92[CHD][hapmap];0.84[GIH][hapmap]
rs12712627	0.92[CHD][hapmap];0.84[GIH][hapmap]
rs12712628	0.84[EUR][1000 genomes]
rs13035182	0.85[EUR][1000 genomes]
rs1901289	0.84[GIH][hapmap]
rs2060743	0.81[CHB][hapmap]
rs2373473	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099940	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3099941	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3099943	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3099945	1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3099948	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3099949	0.82[ASN][1000 genomes]
rs3099957	0.81[AMR][1000 genomes]
rs3099958	0.81[EUR][1000 genomes]
rs3099959	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs3099998	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3112170	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3112172	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs373300	0.89[GIH][hapmap]
rs4670268	0.81[EUR][1000 genomes]
rs4670899	0.81[CHB][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs6544180	0.85[EUR][1000 genomes]
rs6706091	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs6738069	0.91[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs6744514	0.82[CEU][hapmap];0.80[CHB][hapmap];0.85[EUR][1000 genomes]
rs6754902	0.83[EUR][1000 genomes]
rs7598922	0.84[GIH][hapmap]
rs9808136	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv2692	chr2:39065768-39111871	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3099942	DHX57	Cis_1M	lymphoblastoid	RTeQTL
rs3099942	ITGB1	trans	parietal	SCAN
rs3099942	MORN2	cis	parietal	SCAN
rs3099942	DHX57	cis	cerebellum	SCAN
rs3099942	DHX57	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39038800-39102200	Weak transcription	Gastric	stomach
2	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
4	chr2:39080000-39102200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:39081200-39102200	Weak transcription	Right Ventricle	heart
6	chr2:39081200-39102200	Weak transcription	Spleen	Spleen
7	chr2:39081200-39102400	Weak transcription	Pancreas	Pancrea
8	chr2:39086400-39101800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:39088200-39102000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr2:39089200-39101800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:39089200-39101800	Weak transcription	Fetal Heart	heart
12	chr2:39089400-39101200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:39089400-39102000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:39089400-39102200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:39089400-39102200	Weak transcription	Ovary	ovary
16	chr2:39089400-39102200	Weak transcription	Small Intestine	intestine
17	chr2:39089600-39101800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:39089600-39102000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:39089600-39102000	Weak transcription	NHLF	lung
20	chr2:39089600-39102400	Weak transcription	Lung	lung
21	chr2:39089800-39101800	Weak transcription	Brain Substantia Nigra	brain
22	chr2:39090000-39102000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr2:39090000-39102000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:39090200-39101800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:39090200-39102400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr2:39090400-39099400	Weak transcription	K562	blood
27	chr2:39090600-39101800	Weak transcription	HUVEC	blood vessel
28	chr2:39090600-39101800	Weak transcription	Osteobl	bone
29	chr2:39090600-39102000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:39090600-39102000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr2:39090600-39102200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr2:39090800-39102000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:39090800-39102000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:39090800-39102000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:39090800-39102000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:39090800-39102000	Weak transcription	Adipose Nuclei	Adipose
37	chr2:39090800-39102000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr2:39090800-39102000	Weak transcription	HSMMtube	muscle
39	chr2:39090800-39102000	Weak transcription	NHDF-Ad	bronchial
40	chr2:39092000-39102200	Weak transcription	Right Atrium	heart
41	chr2:39092800-39102200	Weak transcription	Psoas Muscle	Psoas
42	chr2:39093800-39101800	Weak transcription	NH-A	brain
43	chr2:39094200-39101800	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr2:39094200-39102000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr2:39094200-39102400	Weak transcription	Aorta	Aorta
46	chr2:39094400-39098600	Weak transcription	Fetal Stomach	stomach
47	chr2:39094400-39100800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:39094400-39102000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:39094400-39102000	Weak transcription	Liver	Liver
50	chr2:39094400-39102000	Weak transcription	Brain Hippocampus Middle	brain

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