Variant report

Variant	rs6774276
Chromosome Location	chr3:160941318-160941319
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:160941297-160941325	MCF-7	breast:	n/a	n/a
2	POLR2A	chr3:160941098-160941392	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
2	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
3	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
4	chr3:160472482..160474998-chr3:160940275..160941880,2	MCF-7	breast:
5	chr3:160940674..160943053-chr3:161145134..161148083,2	MCF-7	breast:
6	chr3:160940058..160942666-chr3:161042036..161044035,3	MCF-7	breast:

No data

Variant related genes	Relation type
NMD3	TF binding region
ENSG00000271052	TF binding region
ENSG00000163590	Chromatin interaction
ENSG00000240138	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000169255	Chromatin interaction
ENSG00000269888	Chromatin interaction
ENSG00000260572	Chromatin interaction
ENSG00000234851	Chromatin interaction
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1037888	1.00[JPT][hapmap]
rs10804790	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1154701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12486253	0.85[EUR][1000 genomes]
rs12493960	0.88[AMR][1000 genomes]
rs12495310	0.86[EUR][1000 genomes]
rs13083229	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs1382427	0.85[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1382428	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1478565	0.85[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1478568	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1599374	1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs1599376	0.88[AMR][1000 genomes]
rs1599378	0.88[AMR][1000 genomes]
rs1600209	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1609688	0.88[AMR][1000 genomes]
rs163327	1.00[JPT][hapmap]
rs163328	0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs189270	0.85[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1993891	0.85[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2404340	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28515190	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs336541	0.86[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs336543	0.85[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs336548	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs336567	0.86[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs336568	0.83[EUR][1000 genomes]
rs336569	0.82[AMR][1000 genomes]
rs336570	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs336572	0.80[CEU][hapmap]
rs336577	0.86[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs336580	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs336582	0.83[EUR][1000 genomes]
rs336583	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs336585	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs336586	0.89[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs336589	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs336590	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs336591	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs336593	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs339101	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs3849524	0.85[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4273380	0.86[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4290817	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs4350933	0.87[EUR][1000 genomes]
rs4370045	0.85[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4414866	1.00[JPT][hapmap];0.91[AMR][1000 genomes]
rs4470535	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4493448	0.86[EUR][1000 genomes]
rs4493449	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs4518145	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4560315	0.86[EUR][1000 genomes]
rs456611	0.85[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs459515	0.81[EUR][1000 genomes]
rs459697	0.85[AMR][1000 genomes]
rs4597724	0.85[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs460508	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs462514	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs463928	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs464766	0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs4856714	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs4856738	0.86[EUR][1000 genomes]
rs4856739	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4856767	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs4856768	0.85[EUR][1000 genomes]
rs5004752	1.00[JPT][hapmap]
rs55688744	0.88[EUR][1000 genomes]
rs6441370	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441371	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6441373	0.86[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6762645	1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6765269	0.86[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6765270	0.88[AMR][1000 genomes]
rs6768818	0.88[EUR][1000 genomes]
rs6775627	0.84[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6789388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791213	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6794601	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs6809256	0.82[EUR][1000 genomes]
rs7611367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7613227	0.80[EUR][1000 genomes]
rs7613358	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs7615592	0.86[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7622047	1.00[JPT][hapmap]
rs7623206	0.86[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7627528	0.85[EUR][1000 genomes]
rs7629987	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7632797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7633186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7636941	0.83[EUR][1000 genomes]
rs7638668	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7647327	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7652267	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs7653233	0.85[EUR][1000 genomes]
rs7653361	0.86[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs898680	1.00[JPT][hapmap]
rs899275	0.82[EUR][1000 genomes]
rs9290065	1.00[JPT][hapmap]
rs9290073	0.87[EUR][1000 genomes]
rs9290074	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs975323	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9790314	0.85[EUR][1000 genomes]
rs9809522	0.86[EUR][1000 genomes]
rs980975	1.00[JPT][hapmap]
rs980976	1.00[JPT][hapmap]
rs9815222	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs9821201	0.86[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9831488	1.00[JPT][hapmap]
rs9834659	0.86[EUR][1000 genomes]
rs9839527	0.85[EUR][1000 genomes]
rs9846756	0.99[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9847866	1.00[JPT][hapmap]
rs9850455	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs9860360	1.00[JPT][hapmap]
rs9864752	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs9870059	0.82[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9872514	0.86[CEU][hapmap];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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6774276	SPTSSB	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160938400-160941400	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr3:160938400-160941600	Active TSS	Stomach Smooth Muscle	stomach
3	chr3:160938600-160941400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:160938600-160941400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:160938600-160941600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr3:160938600-160941600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:160938600-160941600	Active TSS	NHLF	lung
8	chr3:160938600-160942400	Active TSS	Right Ventricle	heart
9	chr3:160939800-160995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:160940000-160941400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr3:160940000-160941600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr3:160940000-160942400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr3:160940000-160971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:160940000-160977400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:160940200-160941400	Flanking Active TSS	Dnd41	blood
16	chr3:160940200-160941600	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr3:160940200-160941600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:160940200-160941800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr3:160940200-160942800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:160940200-160943800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:160940200-160965400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:160940400-160941400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
23	chr3:160940400-160941400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:160940400-160941400	Flanking Active TSS	Hela-S3	cervix
25	chr3:160940400-160942000	Flanking Active TSS	HUVEC	blood vessel
26	chr3:160940400-160942200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:160940400-160943000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr3:160940600-160941400	Flanking Active TSS	NHEK	skin
29	chr3:160940600-160941600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
30	chr3:160940600-160941800	Transcr. at gene 5' and 3'	A549	lung
31	chr3:160940600-160942200	Transcr. at gene 5' and 3'	K562	blood
32	chr3:160940800-160941400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:160940800-160941400	Enhancers	Fetal Heart	heart
34	chr3:160940800-160941600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
35	chr3:160940800-160941600	Active TSS	Colon Smooth Muscle	Colon
36	chr3:160940800-160941600	Active TSS	HepG2	liver
37	chr3:160940800-160941800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:160940800-160941800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr3:160940800-160941800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr3:160940800-160941800	Enhancers	Fetal Brain Male	brain
41	chr3:160940800-160942000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr3:160940800-160942000	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr3:160940800-160942000	Active TSS	HMEC	breast
44	chr3:160940800-160942200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:160940800-160942800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:160940800-160946600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr3:160940800-160946600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr3:160940800-160956000	Weak transcription	Colonic Mucosa	Colon
49	chr3:160941000-160941400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:160941000-160941400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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