Variant report

Variant	rs4689863
Chromosome Location	chr4:7788681-7788682
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:91414030..91415040-chr4:7788215..7789214,4	HCT-116	colon:
2	chr4:7787308..7789396-chr4:7796554..7799014,2	K562	blood:
3	chr4:7783261..7784863-chr4:7786642..7789248,2	K562	blood:
4	chr4:7785064..7787531-chr4:7788291..7790828,3	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10516189	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723068	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11724590	0.85[CHB][hapmap]
rs11725132	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11725213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11727624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11728415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11731614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11736326	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11736912	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11737451	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16841112	0.89[CEU][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes]
rs16841187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16841215	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841246	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017177	0.91[AMR][1000 genomes]
rs2240053	0.89[CEU][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs2240054	0.89[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap]
rs2240055	0.91[AMR][1000 genomes]
rs2269849	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2269878	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276967	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]
rs2285766	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2285767	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2285769	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2285770	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2285771	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]
rs2285772	0.85[ASN][1000 genomes]
rs28604598	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4538480	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4689162	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4689165	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4689862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4997103	0.89[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes]
rs55677626	0.88[AMR][1000 genomes]
rs55752670	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55817815	0.84[AMR][1000 genomes]
rs58790280	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58957020	0.91[AMR][1000 genomes]
rs67476190	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67725344	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6852934	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs757252	0.91[AMR][1000 genomes]
rs7660919	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7695250	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	nsv1006642	chr4:7786980-7811291	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4689863	AICDA	trans	lymphoblastoid	seeQTL
rs4689863	STAG3	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7758400-7795400	Weak transcription	Hela-S3	cervix
2	chr4:7759400-7790400	Weak transcription	Psoas Muscle	Psoas
3	chr4:7762000-7805800	Weak transcription	Stomach Mucosa	stomach
4	chr4:7770800-7828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:7776400-7790000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:7776400-7799000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:7776400-7800000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr4:7776400-7806800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:7780200-7794400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:7780600-7800200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr4:7780800-7790600	Weak transcription	Pancreas	Pancrea
12	chr4:7781000-7800000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr4:7781200-7796000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:7781400-7800400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:7781400-7801000	Weak transcription	Brain Substantia Nigra	brain
16	chr4:7781400-7801200	Weak transcription	Brain Anterior Caudate	brain
17	chr4:7781600-7789400	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr4:7781600-7791400	Strong transcription	Fetal Intestine Large	intestine
19	chr4:7781600-7807400	Weak transcription	Brain Angular Gyrus	brain
20	chr4:7781800-7790000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:7782000-7790600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:7782200-7791000	Strong transcription	Stomach Smooth Muscle	stomach
23	chr4:7782600-7790800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr4:7783400-7794000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:7783400-7798800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:7783400-7799200	Weak transcription	HepG2	liver
27	chr4:7783600-7789200	Strong transcription	HSMM	muscle
28	chr4:7783800-7806200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr4:7784000-7791000	Weak transcription	Spleen	Spleen
30	chr4:7784000-7792800	Weak transcription	Primary T cells from cord blood	blood
31	chr4:7784000-7794200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:7784000-7794400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:7784000-7801800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr4:7784000-7821200	Weak transcription	Small Intestine	intestine
35	chr4:7784200-7788800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:7784200-7790600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr4:7784200-7797800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:7784200-7800600	Weak transcription	Brain Hippocampus Middle	brain
39	chr4:7784200-7800600	Weak transcription	Esophagus	oesophagus
40	chr4:7784200-7802200	Weak transcription	Aorta	Aorta
41	chr4:7784200-7802800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr4:7784400-7791800	Strong transcription	Fetal Stomach	stomach
43	chr4:7784400-7794000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:7784600-7791400	Strong transcription	A549	lung
45	chr4:7784800-7789200	Strong transcription	Fetal Lung	lung
46	chr4:7784800-7789400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:7784800-7791400	Strong transcription	NHLF	lung
48	chr4:7784800-7792800	Strong transcription	NH-A	brain
49	chr4:7784800-7803400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:7785000-7789000	Genic enhancers	HUVEC	blood vessel

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