Variant report

Variant	rs17365015
Chromosome Location	chr2:10933024-10933025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10924985..10929288-chr2:10932246..10936170,4	MCF-7	breast:
2	chr2:10927095..10928984-chr2:10930437..10933436,3	K562	blood:
3	chr2:10928919..10935685-chr2:10937600..10943816,9	K562	blood:
4	chr2:10932697..10935521-chr2:10952889..10955116,2	K562	blood:
5	chr2:10931309..10945449-chr2:10946731..10956927,22	K562	blood:
6	chr2:10930748..10933243-chr2:10936511..10939337,3	K562	blood:

Variant related genes	Relation type
ENSG00000143870	Chromatin interaction
ENSG00000238962	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10182400	0.92[EUR][1000 genomes]
rs10192112	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs10197595	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10200007	0.90[EUR][1000 genomes]
rs10520049	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];1.00[ASN][1000 genomes]
rs11489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes]
rs11683190	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11686660	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11885932	0.82[EUR][1000 genomes]
rs12617247	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12617440	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs13404780	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13415153	1.00[CHB][hapmap]
rs1387568	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17364770	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17364812	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17365299	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17455729	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17455876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029426	1.00[CHB][hapmap]
rs2357816	0.89[EUR][1000 genomes]
rs3856467	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4669616	1.00[CHB][hapmap]
rs6714903	0.99[EUR][1000 genomes]
rs6718547	0.99[EUR][1000 genomes]
rs6722515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733037	0.86[EUR][1000 genomes]
rs6756520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs6756672	1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs73174526	0.90[EUR][1000 genomes]
rs7561135	0.92[EUR][1000 genomes]
rs7570179	0.92[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	nsv1000731	chr2:10758657-10943882	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv580968	chr2:10923268-10933249	Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17365015	PDIA6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10915600-10939800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:10915600-10950400	Weak transcription	Right Atrium	heart
3	chr2:10916200-10939200	Strong transcription	Fetal Stomach	stomach
4	chr2:10916400-10938600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:10916600-10943800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr2:10916800-10933800	Strong transcription	Spleen	Spleen
7	chr2:10916800-10937400	Strong transcription	Lung	lung
8	chr2:10916800-10942400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:10917000-10933600	Strong transcription	Primary T cells from cord blood	blood
10	chr2:10917000-10939400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:10917200-10933400	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:10917200-10933400	Strong transcription	NHLF	lung
13	chr2:10917200-10934200	Strong transcription	Adipose Nuclei	Adipose
14	chr2:10917200-10937800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr2:10917200-10937800	Strong transcription	Thymus	Thymus
16	chr2:10917200-10939000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:10917200-10942800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:10917200-10943200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:10917200-10943200	Strong transcription	Fetal Thymus	thymus
20	chr2:10917400-10941200	Strong transcription	Liver	Liver
21	chr2:10917400-10942400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr2:10917600-10939200	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:10917600-10943200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:10917600-10943200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:10917600-10943200	Strong transcription	Fetal Muscle Leg	muscle
26	chr2:10917800-10937800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:10917800-10942800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:10917800-10943200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:10917800-10943200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr2:10917800-10943200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:10917800-10944400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:10918000-10938200	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr2:10918000-10942400	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr2:10918000-10942600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:10918200-10933400	Strong transcription	Brain Cingulate Gyrus	brain
36	chr2:10918200-10934200	Strong transcription	Dnd41	blood
37	chr2:10918200-10937800	Strong transcription	Ovary	ovary
38	chr2:10918200-10938000	Strong transcription	Primary B cells from cord blood	blood
39	chr2:10918200-10942200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:10918200-10942600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr2:10918200-10943200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr2:10918400-10943200	Strong transcription	HSMM	muscle
43	chr2:10918600-10933400	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr2:10918600-10942400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:10919600-10943800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:10919800-10934200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr2:10919800-10939400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr2:10919800-10942400	Strong transcription	Osteobl	bone
49	chr2:10920000-10933200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:10920000-10933400	Strong transcription	Fetal Lung	lung

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