Variant report

Variant	rs7649954
Chromosome Location	chr3:160785165-160785166
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160776732..160778669-chr3:160784922..160787021,2	MCF-7	breast:
2	chr3:160783848..160785805-chr3:160786120..160789700,3	MCF-7	breast:
3	chr3:160783790..160785578-chr3:161057040..161058658,2	MCF-7	breast:
4	chr3:160784766..160787646-chr3:161137298..161141604,4	MCF-7	breast:
5	chr3:160748438..160750159-chr3:160785119..160786787,2	MCF-7	breast:
6	chr3:160784979..160786656-chr3:160985367..160987693,2	MCF-7	breast:
7	chr3:160783004..160785203-chr3:160947837..160949834,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1045448	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11922296	0.85[CEU][hapmap]
rs12107243	0.95[CEU][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12488621	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12494133	0.90[CEU][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12494844	0.81[TSI][hapmap]
rs13318781	0.81[TSI][hapmap]
rs13319969	0.95[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs13325518	0.85[CEU][hapmap]
rs1348976	0.87[CEU][hapmap]
rs1374789	0.83[CEU][hapmap]
rs1374790	0.83[CEU][hapmap]
rs1447615	0.85[CEU][hapmap]
rs1599380	0.87[EUR][1000 genomes]
rs1599384	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs16831850	0.81[LWK][hapmap];0.87[MKK][hapmap]
rs16831853	0.81[LWK][hapmap];0.83[MKK][hapmap]
rs16831868	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1839018	0.85[CEU][hapmap]
rs1947686	0.95[CEU][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs2231252	0.93[ASW][hapmap];0.95[CEU][hapmap];0.85[LWK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2279106	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28623696	0.97[EUR][1000 genomes]
rs35440670	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs35599916	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4339146	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4443220	0.95[CEU][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs4465984	0.89[CEU][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs6441350	0.81[LWK][hapmap];0.87[MKK][hapmap]
rs6441352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441353	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs6763838	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6795977	0.93[ASW][hapmap];0.95[CEU][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs6796168	0.84[MKK][hapmap]
rs6801330	0.85[CEU][hapmap]
rs68159406	0.87[EUR][1000 genomes]
rs721657	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs731363	0.84[TSI][hapmap]
rs7429731	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7630896	1.00[CEU][hapmap];0.81[YRI][hapmap];0.87[EUR][1000 genomes]
rs7634115	0.87[EUR][1000 genomes]
rs898683	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs898684	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs898685	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9813136	0.81[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9824308	0.93[ASW][hapmap];0.90[CEU][hapmap];0.81[LWK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9829882	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9830139	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9834751	0.87[EUR][1000 genomes]
rs9840389	0.88[EUR][1000 genomes]
rs9851292	0.84[EUR][1000 genomes]
rs9861850	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9864145	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7649954	B3GALNT1	cis	Artery Tibial	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160768000-160786400	Weak transcription	Left Ventricle	heart
2	chr3:160773200-160786800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:160773600-160785600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:160773800-160787200	Weak transcription	Gastric	stomach
5	chr3:160776000-160787200	Weak transcription	Brain Angular Gyrus	brain
6	chr3:160777200-160787800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:160778200-160786400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:160779200-160785200	Weak transcription	Aorta	Aorta
9	chr3:160780400-160788600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:160780600-160786400	Weak transcription	Primary T cells from cord blood	blood
11	chr3:160780800-160821400	Weak transcription	Fetal Brain Male	brain
12	chr3:160781200-160786600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr3:160781400-160785400	Weak transcription	Pancreas	Pancrea
14	chr3:160781400-160803400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:160781600-160788000	Weak transcription	Psoas Muscle	Psoas
16	chr3:160781600-160791000	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:160781800-160787200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:160781800-160787400	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:160781800-160798200	Weak transcription	Fetal Stomach	stomach
20	chr3:160781800-160822000	Weak transcription	Thymus	Thymus
21	chr3:160782000-160799800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:160782200-160785200	Weak transcription	Adipose Nuclei	Adipose
23	chr3:160782600-160785600	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:160782600-160786400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:160782600-160787200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:160782800-160795000	Weak transcription	Right Ventricle	heart
27	chr3:160783200-160787200	Weak transcription	Fetal Intestine Small	intestine
28	chr3:160783400-160787200	Weak transcription	Fetal Thymus	thymus
29	chr3:160783400-160787400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:160783400-160787400	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:160783400-160788600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:160783800-160787200	Weak transcription	Fetal Brain Female	brain
33	chr3:160784000-160785400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:160784000-160787000	Weak transcription	Brain Germinal Matrix	brain
35	chr3:160784000-160787200	Weak transcription	Esophagus	oesophagus
36	chr3:160784000-160789400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:160784200-160787200	Enhancers	Primary B cells from cord blood	blood
38	chr3:160784200-160799000	Weak transcription	Ovary	ovary
39	chr3:160784400-160788800	Enhancers	Primary B cells from peripheral blood	blood
40	chr3:160784600-160785400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr3:160784600-160786200	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr3:160785000-160786800	Enhancers	Fetal Heart	heart
43	chr3:160785000-160786800	Enhancers	GM12878-XiMat	blood
44	chr3:160785000-160789000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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