Variant report

Variant	rs4145374
Chromosome Location	chr2:9903788-9903789
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9695083..9696978-chr2:9901909..9904289,2	K562	blood:
2	chr2:9901768..9906137-chr2:9907161..9912624,7	K562	blood:
3	chr2:9902911..9905269-chr2:9908747..9910675,2	K562	blood:
4	chr2:9901947..9904351-chr2:9980319..9983166,2	K562	blood:
5	chr2:9897831..9899412-chr2:9902196..9904626,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151694	Chromatin interaction
ENSG00000271855	Chromatin interaction
ENSG00000243491	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10189991	0.85[CEU][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs11889675	0.85[CEU][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs12329266	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12619723	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13393165	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs13406396	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13412895	0.85[CEU][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.83[EUR][1000 genomes]
rs16867150	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16867153	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16867155	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55683574	0.84[EUR][1000 genomes]
rs55831980	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67071207	0.85[EUR][1000 genomes]
rs67169917	0.85[EUR][1000 genomes]
rs72779090	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72779094	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1014911	chr2:9863969-9905959	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv873618	chr2:9870631-9919759	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv873619	chr2:9870631-9956981	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv518227	chr2:9893454-9909114	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4145374	PDIA6	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9895400-9904000	Weak transcription	Hela-S3	cervix
2	chr2:9898600-9904000	Weak transcription	NH-A	brain
3	chr2:9898600-9904400	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:9898600-9905800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:9898600-9906000	Weak transcription	Lung	lung
6	chr2:9898600-9906200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:9898600-9906400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:9898600-9906400	Weak transcription	Placenta	Placenta
9	chr2:9898600-9906800	Enhancers	Fetal Muscle Leg	muscle
10	chr2:9899400-9909200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:9899600-9904800	Weak transcription	Esophagus	oesophagus
12	chr2:9899800-9905200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:9900400-9909400	Weak transcription	Brain Anterior Caudate	brain
14	chr2:9900800-9906200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:9901000-9906000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:9901000-9906000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:9901000-9906000	Weak transcription	HMEC	breast
18	chr2:9901200-9903800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr2:9901200-9903800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:9901200-9904000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr2:9901200-9905800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:9901200-9905800	Weak transcription	NHEK	skin
23	chr2:9901200-9906800	Enhancers	Fetal Heart	heart
24	chr2:9901400-9904000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:9901400-9904000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:9901400-9904600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:9901400-9906200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:9901400-9909400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:9901400-9909400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:9901600-9906200	Weak transcription	Fetal Thymus	thymus
31	chr2:9901800-9910200	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:9902000-9906000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:9902200-9905800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:9902200-9906000	Weak transcription	Fetal Lung	lung
35	chr2:9902200-9906200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:9902400-9904000	Weak transcription	Primary B cells from cord blood	blood
37	chr2:9902400-9906000	Weak transcription	Fetal Brain Male	brain
38	chr2:9902600-9905200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:9903000-9904800	Enhancers	Pancreas	Pancrea
40	chr2:9903000-9911800	Enhancers	Fetal Intestine Small	intestine
41	chr2:9903200-9903800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:9903200-9903800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr2:9903200-9903800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr2:9903200-9904200	Enhancers	Pancreatic Islets	Pancreatic Islet
45	chr2:9903200-9905000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr2:9903200-9906200	Enhancers	K562	blood
47	chr2:9903200-9912000	Enhancers	Fetal Intestine Large	intestine
48	chr2:9903400-9904600	Bivalent Enhancer	HepG2	liver
49	chr2:9903600-9904200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr2:9903600-9904400	Enhancers	Osteobl	bone

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