Variant report

Variant	rs13071892
Chromosome Location	chr3:160817877-160817878
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160816932..160819441-chr3:160937058..160940131,3	MCF-7	breast:
2	chr3:160786642..160788388-chr3:160816154..160818351,2	MCF-7	breast:
3	chr3:160814540..160818049-chr3:161087741..161090722,3	MCF-7	breast:
4	chr3:160817299..160817938-chr3:160887095..160887810,2	MCF-7	breast:
5	chr3:160813033..160824577-chr3:161083489..161092050,35	MCF-7	breast:
6	chr3:160815084..160818315-chr3:161137399..161140050,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10154889	0.85[AMR][1000 genomes]
rs10433352	0.86[AMR][1000 genomes]
rs11712713	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11715733	0.86[AMR][1000 genomes]
rs11717272	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11720263	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11915989	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11922957	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11922959	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12696112	0.82[AMR][1000 genomes]
rs12696113	0.82[AMR][1000 genomes]
rs13060601	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13060718	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13061088	0.94[ASN][1000 genomes]
rs13062651	0.82[AMR][1000 genomes]
rs13085336	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13098896	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13256	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13315565	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1599388	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16831796	0.84[AMR][1000 genomes]
rs16831886	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2014810	0.86[AMR][1000 genomes]
rs34221255	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34630898	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35127376	0.83[EUR][1000 genomes]
rs35589595	0.81[EUR][1000 genomes]
rs35914913	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4494975	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4521287	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4679929	0.84[AMR][1000 genomes]
rs4856700	0.83[EUR][1000 genomes]
rs57145341	0.84[AMR][1000 genomes]
rs6441362	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6772723	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6794882	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6806015	0.91[AMR][1000 genomes]
rs68166680	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73021215	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73023235	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7610432	0.86[AMR][1000 genomes]
rs7618924	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7624185	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7628389	0.85[AMR][1000 genomes]
rs7638370	0.81[EUR][1000 genomes]
rs898677	0.86[AMR][1000 genomes]
rs964533	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9812507	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9822435	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9832109	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9857855	0.86[AMR][1000 genomes]
rs9862086	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9876142	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9880269	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9883566	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	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
2	nsv877704	chr3:160806859-160836006	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13071892	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs13071892	SPTSSB	cis	Adipose Subcutaneous	GTEx
rs13071892	SPTSSB	cis	Thyroid	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160780800-160821400	Weak transcription	Fetal Brain Male	brain
2	chr3:160781800-160822000	Weak transcription	Thymus	Thymus
3	chr3:160787000-160822000	Weak transcription	Primary T cells from cord blood	blood
4	chr3:160787200-160818800	Weak transcription	Brain Germinal Matrix	brain
5	chr3:160789600-160818800	Weak transcription	Esophagus	oesophagus
6	chr3:160796200-160821800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:160797000-160822000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:160798600-160821800	Weak transcription	Brain Angular Gyrus	brain
9	chr3:160799800-160821800	Weak transcription	NHLF	lung
10	chr3:160799800-160822000	Weak transcription	HMEC	breast
11	chr3:160800200-160818200	Weak transcription	Fetal Intestine Small	intestine
12	chr3:160800200-160820000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:160800400-160818800	Weak transcription	Gastric	stomach
14	chr3:160800400-160822200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:160800400-160822400	Weak transcription	Spleen	Spleen
16	chr3:160801000-160821800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:160801200-160822000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:160801600-160818800	Weak transcription	Placenta	Placenta
19	chr3:160801600-160821800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:160802600-160821400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:160802600-160822000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr3:160802600-160822400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:160802800-160822000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:160803400-160819200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:160803400-160822000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:160803800-160822000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:160804400-160818200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:160804400-160822000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:160804400-160822000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:160804600-160820400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:160804600-160821800	Weak transcription	Brain Substantia Nigra	brain
32	chr3:160804600-160821800	Weak transcription	HUVEC	blood vessel
33	chr3:160804600-160822200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:160805800-160818800	Weak transcription	Lung	lung
35	chr3:160807000-160818800	Weak transcription	Fetal Kidney	kidney
36	chr3:160807800-160818800	Weak transcription	Adipose Nuclei	Adipose
37	chr3:160807800-160820200	Weak transcription	Pancreas	Pancrea
38	chr3:160809000-160821800	Weak transcription	NHDF-Ad	bronchial
39	chr3:160809000-160822200	Weak transcription	Psoas Muscle	Psoas
40	chr3:160813400-160818800	Weak transcription	Right Atrium	heart
41	chr3:160813400-160822000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr3:160813600-160818000	Weak transcription	Fetal Intestine Large	intestine
43	chr3:160813800-160818800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:160814000-160821600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:160814600-160820800	Strong transcription	Fetal Muscle Leg	muscle
46	chr3:160815200-160820800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:160815200-160820800	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr3:160815600-160821400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:160815800-160820800	Strong transcription	Fetal Lung	lung
50	chr3:160816000-160819800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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