Variant report

Variant	rs34972965
Chromosome Location	chr3:160984296-160984297
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160980523..160999163-chr3:161073509..161094838,104	MCF-7	breast:
2	chr3:160973015..160975782-chr3:160983257..160984865,2	MCF-7	breast:
3	chr3:160977108..160997706-chr3:161077424..161093939,169	MCF-7	breast:
4	chr3:160936882..160947576-chr3:160982516..160994324,28	MCF-7	breast:
5	chr3:160979328..160995719-chr3:161119748..161144811,174	MCF-7	breast:
6	chr3:160982688..160996909-chr3:161122010..161144833,109	MCF-7	breast:
7	chr3:160820825..160823286-chr3:160983994..160987478,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction
ENSG00000240567	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10513564	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11710489	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11711413	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11711695	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11715591	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11718905	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11929238	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13059340	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13059386	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13062740	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13073147	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13076251	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13084731	0.81[EUR][1000 genomes]
rs13084746	0.81[EUR][1000 genomes]
rs1382429	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1450522	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1450523	0.81[EUR][1000 genomes]
rs1478566	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16832082	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2054710	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2100238	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2404341	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2404342	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28384382	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34016896	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34771618	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34896809	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35100811	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35127376	0.80[AMR][1000 genomes]
rs35310734	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35462273	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35589595	0.84[AMR][1000 genomes]
rs4493447	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4856700	0.80[AMR][1000 genomes]
rs4856703	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4856756	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4856757	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4856769	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60625846	0.81[EUR][1000 genomes]
rs6441374	0.84[AMR][1000 genomes]
rs66508859	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67460515	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6780536	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73026974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73026976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7610800	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7610985	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7630356	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7638370	0.80[AMR][1000 genomes]
rs7647118	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7647374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7648279	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9844862	0.81[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	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs34972965	SPTSSB	cis	Nerve Tibial	GTEx
rs34972965	SPTSSB	cis	Adipose Subcutaneous	GTEx
rs34972965	SPTSSB	cis	Thyroid	GTEx
rs34972965	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL
rs34972965	SPTSSB	cis	Heart Left Ventricle	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160939800-160995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:160941000-160984600	Weak transcription	Small Intestine	intestine
3	chr3:160941000-160993400	Weak transcription	Pancreas	Pancrea
4	chr3:160956400-160993000	Weak transcription	Esophagus	oesophagus
5	chr3:160966200-160987400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:160966200-160993200	Weak transcription	Right Ventricle	heart
7	chr3:160968800-160992200	Weak transcription	Brain Angular Gyrus	brain
8	chr3:160970400-160995600	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:160970800-160995600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:160971000-160987400	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:160971000-160989000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:160971000-160993800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:160971000-160995400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:160971000-160995400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:160971200-160984400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr3:160971200-160988800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:160971200-160995200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:160971200-160996000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:160971800-160993000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr3:160972200-160996600	Weak transcription	Brain Substantia Nigra	brain
21	chr3:160972400-160993800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr3:160972600-160984400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:160972800-160995400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:160973200-160984600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr3:160973200-160993200	Weak transcription	Gastric	stomach
26	chr3:160973400-160989000	Weak transcription	Fetal Thymus	thymus
27	chr3:160974600-160990000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:160975400-160995800	Weak transcription	Fetal Intestine Large	intestine
29	chr3:160976400-160985400	Weak transcription	Fetal Lung	lung
30	chr3:160976400-160989400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr3:160976600-160989200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:160976600-160995400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:160976800-160991800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:160978000-160984800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:160979200-160999800	Weak transcription	Psoas Muscle	Psoas
36	chr3:160980200-160985200	Enhancers	NHDF-Ad	bronchial
37	chr3:160981000-160993600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr3:160981200-160990600	Weak transcription	HSMMtube	muscle
39	chr3:160981400-160984600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:160981600-160984400	Weak transcription	Fetal Heart	heart
41	chr3:160982200-160989200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:160982200-160993000	Weak transcription	Ovary	ovary
43	chr3:160982200-160993400	Weak transcription	Lung	lung
44	chr3:160982200-160993400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:160982200-160994000	Weak transcription	Fetal Brain Female	brain
46	chr3:160982200-160994200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:160982200-160994400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:160982200-160994600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:160982200-160995000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr3:160982200-160995400	Weak transcription	Aorta	Aorta

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