Variant report

Variant	rs2276967
Chromosome Location	chr4:7774610-7774611
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	chr4:7754937..7756768-chr4:7773872..7775799,2	K562	blood:
2	chr4:7773384..7775813-chr4:7806131..7807839,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SORCS2-1	chr4:7773931-7776364	NONHSAT095064

Variant related genes	Relation type
ENSG00000272620	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10516189	0.87[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11723068	1.00[ASW][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11725132	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11725213	0.81[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11727624	1.00[ASW][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11728415	0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11731614	0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11731850	0.83[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11736326	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11736912	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11737451	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16841112	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs16841187	0.83[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16841215	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16841246	0.84[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2017177	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2240053	0.89[CEU][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes]
rs2240054	0.89[CEU][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap]
rs2240055	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2269849	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2269878	0.87[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2285766	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2285767	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2285769	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2285770	1.00[ASW][hapmap];0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2285771	0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.82[EUR][1000 genomes]
rs2285772	0.82[EUR][1000 genomes]
rs28604598	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4538480	0.84[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4689162	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4689164	1.00[ASW][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4689165	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4689862	0.85[JPT][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4689863	0.83[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4997103	1.00[ASW][hapmap];0.89[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55677626	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs55752670	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55817815	0.89[AMR][1000 genomes]
rs58790280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58848457	0.81[AMR][1000 genomes]
rs58957020	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs67476190	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67725344	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6852934	0.89[CEU][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs757252	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs7660919	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7695250	0.84[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2276967	AICDA	trans	lymphoblastoid	seeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7757600-7779600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr4:7758000-7780800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:7758200-7783200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:7758400-7795400	Weak transcription	Hela-S3	cervix
5	chr4:7758600-7780600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:7759400-7790400	Weak transcription	Psoas Muscle	Psoas
7	chr4:7760000-7783000	Strong transcription	HSMMtube	muscle
8	chr4:7760000-7783200	Strong transcription	HSMM	muscle
9	chr4:7760200-7779400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:7760400-7780400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:7760600-7780000	Weak transcription	Right Atrium	heart
12	chr4:7761000-7780400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:7761200-7781000	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr4:7761400-7784400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:7762000-7788000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
17	chr4:7763000-7775400	Weak transcription	Right Ventricle	heart
18	chr4:7764400-7776400	Strong transcription	Gastric	stomach
19	chr4:7765000-7776600	Strong transcription	Spleen	Spleen
20	chr4:7765000-7780000	Strong transcription	Lung	lung
21	chr4:7766000-7780600	Strong transcription	Osteobl	bone
22	chr4:7766800-7781200	Strong transcription	HUVEC	blood vessel
23	chr4:7767200-7776600	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr4:7767200-7780800	Strong transcription	NH-A	brain
25	chr4:7767600-7781000	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr4:7768200-7776200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:7768200-7777200	Weak transcription	Brain Substantia Nigra	brain
28	chr4:7768400-7775400	Genic enhancers	Fetal Muscle Leg	muscle
29	chr4:7769000-7780200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:7769200-7776400	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr4:7770000-7775600	Genic enhancers	Fetal Stomach	stomach
32	chr4:7770200-7776200	Strong transcription	Fetal Lung	lung
33	chr4:7770400-7776800	Strong transcription	Aorta	Aorta
34	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr4:7771200-7776600	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr4:7771200-7777200	Weak transcription	Brain Hippocampus Middle	brain
37	chr4:7771600-7775400	Genic enhancers	HepG2	liver
38	chr4:7771600-7780800	Strong transcription	Pancreas	Pancrea
39	chr4:7771800-7780200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr4:7772000-7776000	Genic enhancers	Fetal Intestine Large	intestine
41	chr4:7772000-7776000	Genic enhancers	Fetal Intestine Small	intestine
42	chr4:7772000-7783000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr4:7772400-7776600	Strong transcription	Brain Germinal Matrix	brain
44	chr4:7772600-7774800	Strong transcription	Fetal Muscle Trunk	muscle
45	chr4:7772600-7776400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr4:7772800-7775000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:7772800-7775000	Weak transcription	Brain Anterior Caudate	brain
48	chr4:7772800-7775400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:7772800-7775800	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr4:7772800-7778800	Weak transcription	Brain Inferior Temporal Lobe	brain

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