Variant report

Variant	rs12617440
Chromosome Location	chr2:10922027-10922028
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10919808..10922131-chr2:10929132..10931329,2	K562	blood:
2	chr2:10912736..10915766-chr2:10920191..10922104,3	MCF-7	breast:
3	chr2:10918360..10921313-chr2:10922011..10924317,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143882	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10182400	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192112	0.85[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197595	1.00[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200007	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520049	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs11489	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11885932	0.85[EUR][1000 genomes]
rs12617247	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404780	1.00[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1387568	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17364770	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17364812	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17365015	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs17365299	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17455729	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17455876	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2357816	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856467	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714903	0.96[EUR][1000 genomes]
rs6718547	0.96[EUR][1000 genomes]
rs6722515	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6733037	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756520	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6756672	0.80[EUR][1000 genomes]
rs73174526	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561135	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570179	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12617440	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	chr2:10914600-10922400	Weak transcription	Fetal Kidney	kidney
3	chr2:10914600-10931600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:10915200-10923000	Weak transcription	Fetal Brain Male	brain
5	chr2:10915600-10939800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:10915600-10950400	Weak transcription	Right Atrium	heart
7	chr2:10915800-10929000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:10916200-10939200	Strong transcription	Fetal Stomach	stomach
9	chr2:10916400-10922200	Weak transcription	Fetal Heart	heart
10	chr2:10916400-10923200	Weak transcription	NHDF-Ad	bronchial
11	chr2:10916400-10923600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:10916400-10923600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:10916400-10928600	Strong transcription	Fetal Intestine Small	intestine
14	chr2:10916400-10931200	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:10916400-10931600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:10916400-10938600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:10916600-10943800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr2:10916800-10933800	Strong transcription	Spleen	Spleen
19	chr2:10916800-10937400	Strong transcription	Lung	lung
20	chr2:10916800-10942400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:10917000-10926600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:10917000-10930400	Strong transcription	GM12878-XiMat	blood
23	chr2:10917000-10930600	Strong transcription	NHEK	skin
24	chr2:10917000-10933600	Strong transcription	Primary T cells from cord blood	blood
25	chr2:10917000-10939400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:10917200-10925800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:10917200-10929000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr2:10917200-10931000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:10917200-10931000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:10917200-10933400	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:10917200-10933400	Strong transcription	NHLF	lung
32	chr2:10917200-10934200	Strong transcription	Adipose Nuclei	Adipose
33	chr2:10917200-10937800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr2:10917200-10937800	Strong transcription	Thymus	Thymus
35	chr2:10917200-10939000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:10917200-10942800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:10917200-10943200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:10917200-10943200	Strong transcription	Fetal Thymus	thymus
39	chr2:10917400-10924800	Strong transcription	Stomach Smooth Muscle	stomach
40	chr2:10917400-10930400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr2:10917400-10941200	Strong transcription	Liver	Liver
42	chr2:10917400-10942400	Strong transcription	Fetal Muscle Trunk	muscle
43	chr2:10917600-10930400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:10917600-10930600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr2:10917600-10939200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:10917600-10943200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:10917600-10943200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:10917600-10943200	Strong transcription	Fetal Muscle Leg	muscle
49	chr2:10917800-10937800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:10917800-10942800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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