Variant report

Variant	rs7721668
Chromosome Location	chr5:93290995-93290996
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10044641	0.83[ASN][1000 genomes]
rs10057664	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs10061069	0.84[ASN][1000 genomes]
rs1026279	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs1031423	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10866760	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11135394	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11135397	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs11135401	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11948511	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12054831	0.83[CEU][hapmap]
rs12653528	0.83[CEU][hapmap];0.85[TSI][hapmap]
rs13167027	0.84[ASN][1000 genomes]
rs13186432	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1349711	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs1453003	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs17083377	0.83[CEU][hapmap]
rs17083380	0.94[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1901736	0.83[CEU][hapmap]
rs1982439	0.83[CEU][hapmap]
rs2043979	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2045019	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs2045020	0.83[CEU][hapmap];0.90[TSI][hapmap]
rs2045021	0.83[CEU][hapmap]
rs2084916	0.83[CEU][hapmap]
rs2924374	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs35672980	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60375544	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6556833	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6556834	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs6556838	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs6556839	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs6869110	0.94[CEU][hapmap];0.94[CHB][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6879620	0.83[CEU][hapmap]
rs6881815	0.83[CEU][hapmap]
rs7708175	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7713956	0.83[CEU][hapmap];0.82[TSI][hapmap]
rs7727923	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7728825	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7732578	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7733142	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7735009	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7736892	0.83[CEU][hapmap]
rs890738	0.85[ASN][1000 genomes]
rs896729	0.83[CEU][hapmap];0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532196	chr5:92933949-93573527	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv882384	chr5:93136661-93380123	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7721668	GAL	trans	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93194200-93307600	Weak transcription	Left Ventricle	heart
2	chr5:93263200-93326400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:93263400-93303800	Weak transcription	HSMMtube	muscle
4	chr5:93278000-93304800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:93279400-93292000	Weak transcription	Right Ventricle	heart
6	chr5:93281600-93300200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr5:93282000-93291400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr5:93282200-93309600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:93282600-93294000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr5:93282800-93312000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:93283000-93299000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr5:93284400-93292200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:93284400-93300200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:93284600-93297600	Weak transcription	Fetal Thymus	thymus
15	chr5:93284800-93292400	Weak transcription	Thymus	Thymus
16	chr5:93284800-93306400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:93287000-93307600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr5:93287400-93291600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:93287400-93291800	Strong transcription	Primary B cells from cord blood	blood
20	chr5:93287800-93292400	Weak transcription	Gastric	stomach
21	chr5:93287800-93309400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr5:93288000-93293000	Weak transcription	Fetal Kidney	kidney
23	chr5:93288000-93295800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:93288200-93299600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr5:93288400-93293200	Weak transcription	Brain Anterior Caudate	brain
26	chr5:93288600-93291800	Weak transcription	Liver	Liver
27	chr5:93288600-93294600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:93288800-93292000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr5:93289000-93291000	Strong transcription	Fetal Stomach	stomach
30	chr5:93289000-93291600	Weak transcription	Brain Hippocampus Middle	brain
31	chr5:93289000-93292000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:93289000-93292400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr5:93289000-93311200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr5:93289200-93291000	Strong transcription	Fetal Intestine Small	intestine
35	chr5:93289200-93291000	Strong transcription	Ovary	ovary
36	chr5:93289200-93292600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr5:93289400-93291000	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr5:93289400-93292000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr5:93289400-93296000	Weak transcription	Placenta	Placenta
40	chr5:93289600-93291000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr5:93289600-93291000	Strong transcription	Aorta	Aorta
42	chr5:93289600-93291200	Strong transcription	Adipose Nuclei	Adipose
43	chr5:93289600-93291200	Strong transcription	Fetal Muscle Leg	muscle
44	chr5:93289600-93291800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr5:93289800-93291000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr5:93289800-93291800	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr5:93289800-93292000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:93289800-93292200	Weak transcription	Lung	lung
49	chr5:93289800-93292400	Weak transcription	Fetal Brain Male	brain
50	chr5:93290000-93291000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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