Variant report

Variant	rs13029388
Chromosome Location	chr2:39091906-39091907
allele	G/T
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	chr2:39065831..39067433-chr2:39089862..39092131,2	K562	blood:
4	chr2:39082200..39083996-chr2:39090256..39092735,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1010858	0.89[AFR][1000 genomes]
rs10779923	0.83[CHB][hapmap];0.87[JPT][hapmap];0.87[YRI][hapmap]
rs11124651	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11675110	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12373604	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12465365	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12623330	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12712621	0.82[JPT][hapmap]
rs12712625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12712626	0.88[CEU][hapmap];0.80[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12712627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712628	0.89[AFR][1000 genomes]
rs13029406	0.80[JPT][hapmap]
rs1530852	0.80[JPT][hapmap]
rs1530853	0.80[JPT][hapmap]
rs17494315	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1901289	0.81[CEU][hapmap];0.82[CHB][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2060743	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs3099940	0.83[CHB][hapmap]
rs3099941	0.82[CHB][hapmap]
rs3100000	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs3112159	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs3112163	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs373300	0.83[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs3770681	0.81[CEU][hapmap];0.80[JPT][hapmap]
rs3923144	0.87[JPT][hapmap]
rs4133043	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4265996	0.82[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes]
rs4641916	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4670266	0.93[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4670267	0.81[CEU][hapmap];0.89[CHB][hapmap];0.87[YRI][hapmap]
rs4670899	0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs6706091	0.87[YRI][hapmap];0.80[AFR][1000 genomes]
rs6710418	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6732083	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6734584	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6738403	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6741088	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6744514	0.83[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7419616	0.80[JPT][hapmap]
rs7586929	0.82[AMR][1000 genomes]
rs7589162	0.82[CEU][hapmap];0.81[YRI][hapmap]
rs7598922	0.96[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9808136	0.83[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[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
rs13029388	DHX57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 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	chr2:39080000-39092000	Strong transcription	Primary T cells from cord blood	blood
7	chr2:39080000-39102200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:39081200-39102200	Weak transcription	Right Ventricle	heart
9	chr2:39081200-39102200	Weak transcription	Spleen	Spleen
10	chr2:39081200-39102400	Weak transcription	Pancreas	Pancrea
11	chr2:39081600-39093400	Weak transcription	Aorta	Aorta
12	chr2:39086000-39094400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:39086400-39101800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:39087600-39095400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr2:39088200-39102000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:39089200-39101800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:39089200-39101800	Weak transcription	Fetal Heart	heart
18	chr2:39089400-39093200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:39089400-39093200	Weak transcription	NHEK	skin
20	chr2:39089400-39094000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:39089400-39094200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:39089400-39094600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:39089400-39095600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:39089400-39101200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:39089400-39102000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:39089400-39102200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:39089400-39102200	Weak transcription	Ovary	ovary
28	chr2:39089400-39102200	Weak transcription	Small Intestine	intestine
29	chr2:39089600-39092400	Weak transcription	Psoas Muscle	Psoas
30	chr2:39089600-39093200	Weak transcription	NH-A	brain
31	chr2:39089600-39093400	Weak transcription	Fetal Brain Male	brain
32	chr2:39089600-39093800	Weak transcription	Fetal Stomach	stomach
33	chr2:39089600-39094000	Weak transcription	Thymus	Thymus
34	chr2:39089600-39094000	Weak transcription	Hela-S3	cervix
35	chr2:39089600-39094600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:39089600-39101800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:39089600-39102000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr2:39089600-39102000	Weak transcription	NHLF	lung
39	chr2:39089600-39102400	Weak transcription	Lung	lung
40	chr2:39089800-39097200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:39089800-39101800	Weak transcription	Brain Substantia Nigra	brain
42	chr2:39090000-39093400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:39090000-39094200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr2:39090000-39102000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:39090000-39102000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr2:39090200-39092000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:39090200-39093200	Weak transcription	GM12878-XiMat	blood
48	chr2:39090200-39093400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr2:39090200-39094600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:39090200-39101800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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