Variant report

Variant	rs6741088
Chromosome Location	chr2:39096009-39096010
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38977037..38979808-chr2:39095597..39097239,2	K562	blood:
2	chr2:39089505..39093700-chr2:39094409..39098372,5	K562	blood:
3	chr2:39086851..39091387-chr2:39094171..39096771,4	K562	blood:
4	chr2:39094395..39096056-chr2:39119130..39121663,2	K562	blood:
5	chr2:39095857..39098722-chr2:39101020..39103452,2	MCF-7	breast:
6	chr2:39092323..39097069-chr2:39100019..39103136,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188010	Chromatin interaction
ENSG00000225284	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000163214	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1010858	0.89[ASN][1000 genomes]
rs11124651	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11675110	0.91[AMR][1000 genomes]
rs11689954	0.86[AFR][1000 genomes]
rs12373604	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12465365	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12623330	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12712626	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12712627	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13029388	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17494315	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1901289	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2060743	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3100000	0.86[EUR][1000 genomes]
rs3112163	0.85[EUR][1000 genomes]
rs4133043	0.88[ASN][1000 genomes]
rs4265996	0.85[AMR][1000 genomes]
rs4641916	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4670266	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4670899	0.91[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6710418	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6732083	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6734584	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6738403	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744514	0.81[ASN][1000 genomes]
rs7586929	0.87[AMR][1000 genomes]
rs7598922	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9808136	0.81[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6741088	DHX57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

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	chr2:39089800-39097200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr2:39089800-39101800	Weak transcription	Brain Substantia Nigra	brain
23	chr2:39090000-39102000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr2:39090000-39102000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:39090200-39101800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:39090200-39102400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr2:39090400-39099400	Weak transcription	K562	blood
28	chr2:39090600-39097200	Weak transcription	Brain Anterior Caudate	brain
29	chr2:39090600-39101800	Weak transcription	HUVEC	blood vessel
30	chr2:39090600-39101800	Weak transcription	Osteobl	bone
31	chr2:39090600-39102000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:39090600-39102000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr2:39090600-39102200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr2:39090800-39102000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:39090800-39102000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:39090800-39102000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:39090800-39102000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:39090800-39102000	Weak transcription	Adipose Nuclei	Adipose
39	chr2:39090800-39102000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr2:39090800-39102000	Weak transcription	HSMMtube	muscle
41	chr2:39090800-39102000	Weak transcription	NHDF-Ad	bronchial
42	chr2:39092000-39102200	Weak transcription	Right Atrium	heart
43	chr2:39092800-39102200	Weak transcription	Psoas Muscle	Psoas
44	chr2:39093600-39096600	Weak transcription	GM12878-XiMat	blood
45	chr2:39093800-39101800	Weak transcription	NH-A	brain
46	chr2:39094000-39097000	Weak transcription	Dnd41	blood
47	chr2:39094200-39096400	Weak transcription	Fetal Intestine Small	intestine
48	chr2:39094200-39097600	Weak transcription	Fetal Thymus	thymus
49	chr2:39094200-39101800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:39094200-39102000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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