Variant report

Variant	rs6789388
Chromosome Location	chr3:160970437-160970438
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160951586..160954326-chr3:160968656..160971619,2	K562	blood:
2	chr3:160946584..160950136-chr3:160968989..160972696,3	MCF-7	breast:
3	chr3:160970393..160971997-chr3:161083737..161085470,2	MCF-7	breast:
4	chr3:160938087..160941385-chr3:160967882..160971966,4	MCF-7	breast:
5	chr3:160962204..160965974-chr3:160967847..160971324,6	MCF-7	breast:
6	chr3:160970413..160971945-chr3:160972168..160974529,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169251	Chromatin interaction
ENSG00000271052	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs1037888	1.00[JPT][hapmap]
rs10804790	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1154701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12486253	0.88[EUR][1000 genomes]
rs12493960	0.88[AMR][1000 genomes]
rs12495310	0.90[EUR][1000 genomes]
rs13083229	0.96[CEU][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs1382427	0.85[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1382428	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1478565	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1478568	0.96[CEU][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs1599374	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes]
rs1599376	0.88[AMR][1000 genomes]
rs1599378	0.88[AMR][1000 genomes]
rs1600209	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1609688	0.88[AMR][1000 genomes]
rs1610158	0.84[TSI][hapmap]
rs163327	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs163328	0.85[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs189270	0.85[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1993891	0.85[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2306061	0.80[MEX][hapmap];0.80[TSI][hapmap]
rs2404340	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28515190	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs336541	0.85[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs336543	0.85[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs336548	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs336567	0.85[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336568	0.87[EUR][1000 genomes]
rs336569	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336570	0.85[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336572	0.81[CEU][hapmap]
rs336577	0.85[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs336579	0.81[EUR][1000 genomes]
rs336580	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs336582	0.87[EUR][1000 genomes]
rs336583	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336585	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336586	0.89[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs336589	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336590	0.92[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336591	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336593	0.89[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs339101	0.84[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs3849524	0.80[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4273380	0.85[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4290817	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4350933	0.89[EUR][1000 genomes]
rs4370045	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4414866	1.00[JPT][hapmap];0.91[AMR][1000 genomes]
rs4470535	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4493448	0.88[EUR][1000 genomes]
rs4493449	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs4518145	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4560315	0.90[EUR][1000 genomes]
rs456611	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs459515	0.85[EUR][1000 genomes]
rs459697	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4597724	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs460508	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs462514	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs463928	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs464766	0.85[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4856714	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4856738	0.90[EUR][1000 genomes]
rs4856739	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4856767	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4856768	0.89[EUR][1000 genomes]
rs55688744	0.86[EUR][1000 genomes]
rs6441370	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441371	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6441373	0.85[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6762645	1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6765269	0.85[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]
rs6774276	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]
rs6775627	0.81[ASW][hapmap];0.84[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6791213	0.96[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs6794601	0.85[CEU][hapmap];0.85[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs6809256	0.86[EUR][1000 genomes]
rs7611367	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7613227	0.84[EUR][1000 genomes]
rs7613358	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs7615592	0.85[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7622047	1.00[JPT][hapmap]
rs7623206	0.85[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7627528	0.89[EUR][1000 genomes]
rs7629987	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7632797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7633186	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7636941	0.87[EUR][1000 genomes]
rs7638668	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7647327	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7652267	0.96[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs7653233	0.89[EUR][1000 genomes]
rs7653361	0.85[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs898680	1.00[JPT][hapmap]
rs899275	0.85[EUR][1000 genomes]
rs9290065	1.00[JPT][hapmap];0.80[MEX][hapmap]
rs9290073	0.85[EUR][1000 genomes]
rs9290074	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs975323	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9790314	0.89[EUR][1000 genomes]
rs9809522	0.90[EUR][1000 genomes]
rs980975	1.00[JPT][hapmap]
rs980976	1.00[JPT][hapmap]
rs9815222	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs9821201	0.85[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9834659	0.90[EUR][1000 genomes]
rs9839527	0.89[EUR][1000 genomes]
rs9846756	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9850455	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs9864752	0.85[CEU][hapmap]
rs9870059	0.82[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9872514	0.85[CEU][hapmap];0.85[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
rs6789388	SPTSSB	cis	Heart Left Ventricle	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160939800-160995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:160940000-160971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:160940000-160977400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:160941000-160974800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:160941000-160983000	Weak transcription	Spleen	Spleen
6	chr3:160941000-160984600	Weak transcription	Small Intestine	intestine
7	chr3:160941000-160993400	Weak transcription	Pancreas	Pancrea
8	chr3:160941200-160973400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:160941400-160971800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:160941600-160975400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:160941800-160975200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:160942200-160973200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr3:160942400-160975200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:160942600-160971800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:160942600-160972600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:160942600-160973400	Strong transcription	Fetal Thymus	thymus
17	chr3:160942600-160975000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:160942600-160976600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:160942800-160971800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:160942800-160973800	Strong transcription	NH-A	brain
21	chr3:160942800-160978000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:160943600-160977200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:160946400-160972800	Strong transcription	HSMM	muscle
24	chr3:160947200-160972600	Weak transcription	Stomach Mucosa	stomach
25	chr3:160947400-160973600	Strong transcription	HUVEC	blood vessel
26	chr3:160948800-160971600	Weak transcription	Aorta	Aorta
27	chr3:160948800-160978000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:160949200-160971200	Weak transcription	Brain Substantia Nigra	brain
29	chr3:160949800-160971200	Weak transcription	Fetal Heart	heart
30	chr3:160950000-160978000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr3:160950200-160976600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:160950600-160972800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:160950800-160971200	Strong transcription	NHDF-Ad	bronchial
34	chr3:160951000-160976600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:160951400-160973600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr3:160951400-160975200	Strong transcription	Osteobl	bone
37	chr3:160951600-160975000	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr3:160951600-160976600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:160955000-160975400	Strong transcription	Fetal Intestine Large	intestine
40	chr3:160955800-160971800	Strong transcription	Placenta	Placenta
41	chr3:160955800-160972800	Strong transcription	Primary B cells from peripheral blood	blood
42	chr3:160955800-160973400	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr3:160955800-160974600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr3:160956400-160970600	Weak transcription	Lung	lung
45	chr3:160956400-160993000	Weak transcription	Esophagus	oesophagus
46	chr3:160957400-160973200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr3:160958600-160983600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:160959000-160970600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr3:160959600-160973800	Strong transcription	Dnd41	blood
50	chr3:160961000-160970600	Weak transcription	Placenta Amnion	Placenta Amnion

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