Variant report

Variant	rs2240054
Chromosome Location	chr4:7765193-7765194
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	chr4:7762684..7766410-chr4:7766886..7769453,3	MCF-7	breast:
2	chr4:7764728..7766346-chr4:7767900..7769988,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10516189	0.89[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap]
rs11723068	0.85[GIH][hapmap];0.81[JPT][hapmap]
rs11725213	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs11727624	0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap]
rs11728415	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs11731614	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs11731850	0.89[CEU][hapmap];0.88[JPT][hapmap]
rs11737451	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs16841112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16841187	0.89[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap]
rs16841246	0.89[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap]
rs2017177	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240053	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2240055	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269849	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2269878	0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap]
rs2276967	0.89[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs2285766	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs2285767	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs2285769	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.88[EUR][1000 genomes]
rs2285770	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs2285771	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2285772	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4538480	0.85[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap]
rs4689162	1.00[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs4689164	0.89[CEU][hapmap]
rs4689862	0.89[CEU][hapmap];0.85[JPT][hapmap]
rs4689863	0.89[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap]
rs4997103	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55677626	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55752670	0.81[AMR][1000 genomes]
rs55817815	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58848457	0.86[EUR][1000 genomes]
rs58957020	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6852934	1.00[CEU][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs757252	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs757253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7695250	0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878570	chr4:7534603-7836835	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1007319	chr4:7705550-7832097	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv537018	chr4:7705550-7832097	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv878575	chr4:7715181-7767755	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv878577	chr4:7757650-7771201	Genic enhancers Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2240054	AICDA	trans	lymphoblastoid	seeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7746200-7772000	Weak transcription	Brain Anterior Caudate	brain
2	chr4:7749400-7765600	Weak transcription	Fetal Brain Male	brain
3	chr4:7749400-7767000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:7752800-7767400	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:7754200-7765400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr4:7755400-7768400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:7756000-7766000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:7756400-7767800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr4:7756600-7768000	Weak transcription	Brain Angular Gyrus	brain
10	chr4:7757000-7772000	Strong transcription	Brain Germinal Matrix	brain
11	chr4:7757600-7765400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:7757600-7765400	Strong transcription	Osteobl	bone
13	chr4:7757600-7770800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:7757600-7779600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:7757800-7768200	Weak transcription	Fetal Heart	heart
16	chr4:7757800-7768600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:7757800-7772000	Strong transcription	Fetal Intestine Small	intestine
18	chr4:7758000-7780800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr4:7758200-7783200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:7758400-7795400	Weak transcription	Hela-S3	cervix
21	chr4:7758600-7780600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:7759400-7790400	Weak transcription	Psoas Muscle	Psoas
23	chr4:7759800-7771600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:7759800-7773800	Weak transcription	Fetal Kidney	kidney
25	chr4:7760000-7770000	Strong transcription	Fetal Stomach	stomach
26	chr4:7760000-7783000	Strong transcription	HSMMtube	muscle
27	chr4:7760000-7783200	Strong transcription	HSMM	muscle
28	chr4:7760200-7768800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:7760200-7774200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:7760200-7779400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:7760400-7767200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr4:7760400-7768400	Weak transcription	Left Ventricle	heart
33	chr4:7760400-7780400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:7760600-7765400	Strong transcription	HUVEC	blood vessel
35	chr4:7760600-7780000	Weak transcription	Right Atrium	heart
36	chr4:7761000-7767800	Strong transcription	Stomach Smooth Muscle	stomach
37	chr4:7761000-7780400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:7761200-7766000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:7761200-7769800	Weak transcription	Small Intestine	intestine
40	chr4:7761200-7770600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr4:7761200-7772000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:7761200-7781000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:7761400-7765600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:7761400-7773400	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr4:7761400-7784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:7761600-7767800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:7761600-7769200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr4:7761800-7767800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:7761800-7774400	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:7762000-7772000	Strong transcription	Fetal Intestine Large	intestine

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