Variant report

Variant	rs2285771
Chromosome Location	chr4:7761114-7761115
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	chr4:7760394..7761920-chr4:7766669..7769385,2	K562	blood:
2	chr4:7733646..7736526-chr4:7759484..7762368,2	K562	blood:

Variant related genes	Relation type
ENSG00000184985	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10516189	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs11723068	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11725132	0.81[ASN][1000 genomes]
rs11725213	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11727624	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs11728415	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11731614	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11731850	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11737451	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16841112	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16841187	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs16841215	0.86[ASN][1000 genomes]
rs16841246	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs2017177	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2240053	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2240054	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]
rs2240055	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2269849	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2269878	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2276967	0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes]
rs2285766	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285767	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2285769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2285770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4538480	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs4689162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4689164	0.89[CEU][hapmap]
rs4689165	0.83[ASN][1000 genomes]
rs4689853	0.90[ASN][1000 genomes]
rs4689862	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4689863	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs4997103	1.00[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap]
rs55677626	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55752670	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55817815	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58790280	0.86[ASN][1000 genomes]
rs67476190	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67725344	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6852934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757252	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs757253	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7660919	0.82[ASN][1000 genomes]
rs7695250	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]

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
rs2285771	AICDA	trans	lymphoblastoid	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7740200-7765000	Weak transcription	Aorta	Aorta
2	chr4:7740600-7762400	Weak transcription	Pancreas	Pancrea
3	chr4:7746200-7772000	Weak transcription	Brain Anterior Caudate	brain
4	chr4:7747200-7761800	Weak transcription	Colonic Mucosa	Colon
5	chr4:7749400-7765600	Weak transcription	Fetal Brain Male	brain
6	chr4:7749400-7767000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:7752800-7767400	Weak transcription	Brain Hippocampus Middle	brain
8	chr4:7753000-7761200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr4:7754000-7762000	Weak transcription	NHLF	lung
10	chr4:7754200-7765400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:7755400-7763200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr4:7755400-7768400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:7756000-7761400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:7756000-7766000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:7756200-7762200	Weak transcription	NHEK	skin
16	chr4:7756400-7761400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:7756400-7762200	Weak transcription	HMEC	breast
18	chr4:7756400-7767800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:7756600-7764400	Weak transcription	Esophagus	oesophagus
20	chr4:7756600-7768000	Weak transcription	Brain Angular Gyrus	brain
21	chr4:7757000-7772000	Strong transcription	Brain Germinal Matrix	brain
22	chr4:7757600-7764400	Strong transcription	NH-A	brain
23	chr4:7757600-7765400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:7757600-7765400	Strong transcription	Osteobl	bone
25	chr4:7757600-7770800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:7757600-7779600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:7757800-7768200	Weak transcription	Fetal Heart	heart
28	chr4:7757800-7768600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:7757800-7772000	Strong transcription	Fetal Intestine Small	intestine
30	chr4:7758000-7762600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr4:7758000-7780800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr4:7758200-7764600	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr4:7758200-7783200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr4:7758400-7762000	Strong transcription	A549	lung
35	chr4:7758400-7795400	Weak transcription	Hela-S3	cervix
36	chr4:7758600-7761200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:7758600-7761200	Enhancers	Adipose Nuclei	Adipose
38	chr4:7758600-7762000	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr4:7758600-7762200	Enhancers	Colon Smooth Muscle	Colon
40	chr4:7758600-7780600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:7758800-7763200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:7758800-7763600	Weak transcription	NHDF-Ad	bronchial
43	chr4:7759200-7763600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:7759200-7763600	Weak transcription	GM12878-XiMat	blood
45	chr4:7759400-7761800	Weak transcription	Lung	lung
46	chr4:7759400-7762200	Weak transcription	Fetal Brain Female	brain
47	chr4:7759400-7762200	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr4:7759400-7762400	Weak transcription	Gastric	stomach
49	chr4:7759400-7790400	Weak transcription	Psoas Muscle	Psoas
50	chr4:7759600-7762000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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