Variant report

Variant	rs7153
Chromosome Location	chr3:121383297-121383298
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	chr3:121374281..121376977-chr3:121381116..121385045,3	MCF-7	breast:
2	chr3:121378883..121381780-chr3:121382077..121384890,2	K562	blood:

Variant related genes	Relation type
ENSG00000180353	Chromatin interaction
ENSG00000222057	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10049060	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1127412	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1128163	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1169	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs11916169	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11928871	0.80[AMR][1000 genomes]
rs12496318	1.00[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs12634032	1.00[CEU][hapmap]
rs12635865	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1463736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1574115	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1574133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2141487	1.00[CEU][hapmap]
rs3732407	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3732410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772126	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4048699	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4048703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58367397	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6771068	1.00[CEU][hapmap]
rs6791882	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610298	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7623901	1.00[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs7637495	1.00[CEU][hapmap]
rs7647351	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7648340	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7648343	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9808981	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9817818	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9818073	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820511	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9824235	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9824760	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9838301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850439	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9852845	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9874722	1.00[AFR][1000 genomes];1.00[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	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv998740	chr3:121289499-121390271	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
9	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7153	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs7153	STAM2	trans	lymphoblastoid	RTeQTL
rs7153	EAF2	cis	multi-tissue	Pritchard
rs7153	IQCB1	cis	lymphoblastoid	seeQTL
rs7153	EAF2	cis	lymphoblastoid	seeQTL
rs7153	EAF2	cis	cerebellum	SCAN
rs7153	ALG1L	cis	parietal	SCAN
rs7153	IQCB1	cis	parietal	SCAN
rs7153	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs7153	CD86	cis	lymphoblastoid	seeQTL
rs7153	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs7153	IQCB1	cis	cerebellum	SCAN
rs7153	SLC15A2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121371000-121383600	Weak transcription	Hela-S3	cervix
2	chr3:121377000-121383600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:121378000-121388400	Strong transcription	Fetal Stomach	stomach
4	chr3:121379000-121384200	Enhancers	Fetal Heart	heart
5	chr3:121379400-121384600	Weak transcription	Fetal Kidney	kidney
6	chr3:121379400-121402400	Strong transcription	Fetal Intestine Large	intestine
7	chr3:121379800-121384200	Genic enhancers	Fetal Muscle Leg	muscle
8	chr3:121380000-121402600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:121380200-121385200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:121380200-121386200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:121380200-121397000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:121380400-121384600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:121380400-121385400	Weak transcription	K562	blood
14	chr3:121380400-121386800	Strong transcription	Brain Anterior Caudate	brain
15	chr3:121380400-121396400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:121380400-121396800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:121380400-121402400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:121380400-121402800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:121380400-121406600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:121380600-121384600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:121380600-121384800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:121380600-121384800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr3:121380600-121413800	Weak transcription	Stomach Mucosa	stomach
24	chr3:121380800-121385000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:121380800-121386600	Strong transcription	HSMM	muscle
26	chr3:121380800-121389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:121381000-121388200	Strong transcription	Fetal Intestine Small	intestine
28	chr3:121381000-121391400	Strong transcription	GM12878-XiMat	blood
29	chr3:121381000-121401800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:121381000-121403200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:121381400-121388400	Strong transcription	Gastric	stomach
32	chr3:121381400-121389000	Strong transcription	Thymus	Thymus
33	chr3:121381400-121389800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:121381400-121406800	Strong transcription	Duodenum Mucosa	Duodenum
35	chr3:121381600-121384000	Genic enhancers	HSMMtube	muscle
36	chr3:121381600-121384600	Strong transcription	Fetal Lung	lung
37	chr3:121381600-121385000	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr3:121381600-121385400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr3:121381600-121385600	Strong transcription	Colonic Mucosa	Colon
40	chr3:121381600-121386800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:121381600-121386800	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr3:121381600-121387000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:121381600-121387200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:121381600-121387200	Strong transcription	Brain Germinal Matrix	brain
45	chr3:121381600-121387400	Strong transcription	Brain Hippocampus Middle	brain
46	chr3:121381600-121388200	Strong transcription	Lung	lung
47	chr3:121381600-121388400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:121381600-121388600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:121381600-121388800	Strong transcription	Primary hematopoietic stem cells	blood
50	chr3:121381600-121389000	Strong transcription	Fetal Brain Female	brain

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