Variant report

Variant	rs6738403
Chromosome Location	chr2:39093145-39093146
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39060039..39062647-chr2:39091366..39093415,2	K562	blood:
2	chr2:39089505..39093700-chr2:39094409..39098372,5	K562	blood:
3	chr2:39088675..39091170-chr2:39093044..39095216,2	MCF-7	breast:
4	chr2:39092323..39097069-chr2:39100019..39103136,5	MCF-7	breast:

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

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1010858	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11124651	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11675110	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12373604	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12465365	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12623330	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12712626	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12712627	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712628	0.88[AFR][1000 genomes]
rs13029388	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17494315	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1901289	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2060743	0.89[ASN][1000 genomes]
rs3099995	0.83[EUR][1000 genomes]
rs3100000	0.90[EUR][1000 genomes]
rs3112163	0.90[EUR][1000 genomes]
rs390008	0.81[AMR][1000 genomes]
rs4133043	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4265996	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4641916	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4670266	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4670899	0.81[ASN][1000 genomes]
rs6710418	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6732083	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6734584	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6741088	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744514	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7586929	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7598922	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9808136	0.87[AFR][1000 genomes];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
rs6738403	DHX57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:39038800-39102200	Weak transcription	Gastric	stomach
3	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
5	chr2:39072200-39095400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:39080000-39102200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:39081200-39102200	Weak transcription	Right Ventricle	heart
8	chr2:39081200-39102200	Weak transcription	Spleen	Spleen
9	chr2:39081200-39102400	Weak transcription	Pancreas	Pancrea
10	chr2:39081600-39093400	Weak transcription	Aorta	Aorta
11	chr2:39086000-39094400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:39086400-39101800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:39087600-39095400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr2:39088200-39102000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:39089200-39101800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:39089200-39101800	Weak transcription	Fetal Heart	heart
17	chr2:39089400-39093200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:39089400-39093200	Weak transcription	NHEK	skin
19	chr2:39089400-39094000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:39089400-39094200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:39089400-39094600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:39089400-39095600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:39089400-39101200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:39089400-39102000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:39089400-39102200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr2:39089400-39102200	Weak transcription	Ovary	ovary
27	chr2:39089400-39102200	Weak transcription	Small Intestine	intestine
28	chr2:39089600-39093200	Weak transcription	NH-A	brain
29	chr2:39089600-39093400	Weak transcription	Fetal Brain Male	brain
30	chr2:39089600-39093800	Weak transcription	Fetal Stomach	stomach
31	chr2:39089600-39094000	Weak transcription	Thymus	Thymus
32	chr2:39089600-39094000	Weak transcription	Hela-S3	cervix
33	chr2:39089600-39094600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:39089600-39101800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:39089600-39102000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr2:39089600-39102000	Weak transcription	NHLF	lung
37	chr2:39089600-39102400	Weak transcription	Lung	lung
38	chr2:39089800-39097200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:39089800-39101800	Weak transcription	Brain Substantia Nigra	brain
40	chr2:39090000-39093400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr2:39090000-39094200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr2:39090000-39102000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr2:39090000-39102000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr2:39090200-39093200	Weak transcription	GM12878-XiMat	blood
45	chr2:39090200-39093400	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr2:39090200-39094600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:39090200-39101800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:39090200-39102400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr2:39090400-39093400	Weak transcription	Liver	Liver
50	chr2:39090400-39093600	Weak transcription	Fetal Thymus	thymus

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