Variant report

Variant	rs11489
Chromosome Location	chr2:10923581-10923582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10918202..10921722-chr2:10922034..10926005,5	K562	blood:
2	chr2:10918360..10921313-chr2:10922011..10924317,2	MCF-7	breast:
3	chr2:10862241..10864022-chr2:10922262..10923897,2	MCF-7	breast:
4	chr2:10923480..10926875-chr2:10926902..10929913,3	K562	blood:

Variant related genes	Relation type
ENSG00000143882	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10182400	0.90[EUR][1000 genomes]
rs10192112	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs10197595	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10200007	0.89[EUR][1000 genomes]
rs10520049	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	0.81[EUR][1000 genomes]
rs12617247	0.92[EUR][1000 genomes]
rs12617440	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13404780	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs13415153	1.00[CHB][hapmap]
rs1387568	0.92[EUR][1000 genomes]
rs16856645	0.83[YRI][hapmap]
rs17364770	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17364812	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17365015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes]
rs17365299	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17455729	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17455876	0.99[EUR][1000 genomes]
rs2029426	1.00[CHB][hapmap]
rs2357816	0.88[EUR][1000 genomes]
rs3856467	0.94[EUR][1000 genomes]
rs4669616	1.00[CHB][hapmap]
rs6714903	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718547	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6722515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes]
rs6733037	0.85[EUR][1000 genomes]
rs6748808	0.83[YRI][hapmap]
rs6756520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756672	1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs73174526	0.89[EUR][1000 genomes]
rs7561135	0.90[EUR][1000 genomes]
rs7570179	0.90[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
rs11489	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	chr2:10908600-10924400	Weak transcription	Psoas Muscle	Psoas
2	chr2:10914600-10931600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:10915600-10939800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:10915600-10950400	Weak transcription	Right Atrium	heart
5	chr2:10915800-10929000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:10916200-10939200	Strong transcription	Fetal Stomach	stomach
7	chr2:10916400-10923600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:10916400-10923600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:10916400-10928600	Strong transcription	Fetal Intestine Small	intestine
10	chr2:10916400-10931200	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:10916400-10931600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:10916400-10938600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:10916600-10943800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:10916800-10933800	Strong transcription	Spleen	Spleen
15	chr2:10916800-10937400	Strong transcription	Lung	lung
16	chr2:10916800-10942400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:10917000-10926600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:10917000-10930400	Strong transcription	GM12878-XiMat	blood
19	chr2:10917000-10930600	Strong transcription	NHEK	skin
20	chr2:10917000-10933600	Strong transcription	Primary T cells from cord blood	blood
21	chr2:10917000-10939400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:10917200-10925800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:10917200-10929000	Strong transcription	Duodenum Mucosa	Duodenum
24	chr2:10917200-10931000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:10917200-10931000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr2:10917200-10933400	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr2:10917200-10933400	Strong transcription	NHLF	lung
28	chr2:10917200-10934200	Strong transcription	Adipose Nuclei	Adipose
29	chr2:10917200-10937800	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr2:10917200-10937800	Strong transcription	Thymus	Thymus
31	chr2:10917200-10939000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:10917200-10942800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:10917200-10943200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:10917200-10943200	Strong transcription	Fetal Thymus	thymus
35	chr2:10917400-10924800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr2:10917400-10930400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr2:10917400-10941200	Strong transcription	Liver	Liver
38	chr2:10917400-10942400	Strong transcription	Fetal Muscle Trunk	muscle
39	chr2:10917600-10930400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:10917600-10930600	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:10917600-10939200	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr2:10917600-10943200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:10917600-10943200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:10917600-10943200	Strong transcription	Fetal Muscle Leg	muscle
45	chr2:10917800-10937800	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:10917800-10942800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr2:10917800-10943200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:10917800-10943200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr2:10917800-10943200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:10917800-10944400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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