Variant report

Variant	rs2038270
Chromosome Location	chr14:65028881-65028882
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:65026787..65029450-chr14:65030177..65032001,2	K562	blood:
2	chr14:65007240..65009229-chr14:65027926..65029711,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126803	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10138919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040612	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10431708	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10498515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10873175	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11158546	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1256146	0.88[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs1256150	0.85[EUR][1000 genomes]
rs12589307	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12589322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12894050	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12894807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1453005	0.84[EUR][1000 genomes]
rs1901737	0.82[EUR][1000 genomes]
rs2123461	0.92[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2218994	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs34616731	0.82[EUR][1000 genomes]
rs4902288	0.86[EUR][1000 genomes]
rs4902295	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4902296	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4902297	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4902298	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4902299	0.82[CHB][hapmap]
rs7141346	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7148289	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7149152	0.88[CEU][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7156953	0.87[CEU][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7159809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761547	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8003734	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8007313	0.93[ASW][hapmap];0.90[CHB][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs8016170	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8016361	0.88[CEU][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8017407	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8018169	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8022447	0.88[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs926802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9671381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs971736	0.82[CHB][hapmap];0.80[LWK][hapmap];0.81[YRI][hapmap]

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	nsv1049097	chr14:65027753-65202018	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2038270	PLEKHG3	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65021400-65033400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr14:65021600-65047600	Weak transcription	Pancreas	Pancrea
3	chr14:65023400-65033400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr14:65025000-65030200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr14:65027800-65030600	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr14:65028000-65033400	Weak transcription	Psoas Muscle	Psoas
7	chr14:65028200-65030000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:65028200-65030800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr14:65028200-65031600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr14:65028200-65033400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr14:65028200-65033400	Weak transcription	A549	lung
12	chr14:65028200-65039400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr14:65028400-65029200	Weak transcription	Brain Anterior Caudate	brain
14	chr14:65028400-65029200	Enhancers	Placenta	Placenta
15	chr14:65028400-65033400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr14:65028400-65033400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr14:65028600-65029200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr14:65028600-65029400	Enhancers	Adipose Nuclei	Adipose
19	chr14:65028600-65030000	Weak transcription	Brain Angular Gyrus	brain
20	chr14:65028800-65029200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr14:65028800-65029200	Weak transcription	Right Atrium	heart
22	chr14:65028800-65033400	Weak transcription	Hela-S3	cervix

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