Variant report

Variant	rs6789448
Chromosome Location	chr3:157841531-157841532
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:157826605..157829792-chr3:157838040..157843107,6	K562	blood:
2	chr3:157839952..157841696-chr3:157860084..157861712,2	K562	blood:
3	chr3:157840416..157842184-chr3:157852166..157854407,2	MCF-7	breast:
4	chr3:157836454..157837989-chr3:157840263..157841984,2	K562	blood:
5	chr3:157835764..157837989-chr3:157840263..157842524,2	K562	blood:
6	chr3:157838373..157839974-chr3:157841476..157843018,2	K562	blood:

Variant related genes	Relation type
ENSG00000174891	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10470472	0.86[EUR][1000 genomes]
rs1095636	0.87[EUR][1000 genomes]
rs1193511	0.86[EUR][1000 genomes]
rs1193513	0.86[EUR][1000 genomes]
rs1193536	0.86[EUR][1000 genomes]
rs1204957	0.87[EUR][1000 genomes]
rs12485440	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486461	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12696067	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13059066	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13061378	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1581408	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1608100	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1608101	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1609525	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1609526	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1610266	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610267	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610268	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1724666	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1724679	0.87[EUR][1000 genomes]
rs1729998	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1730008	0.85[EUR][1000 genomes]
rs1730029	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1730032	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1730039	0.86[EUR][1000 genomes]
rs1730041	0.85[EUR][1000 genomes]
rs1730044	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1730099	0.88[EUR][1000 genomes]
rs1915935	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2682402	0.87[EUR][1000 genomes]
rs2682407	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2693540	0.87[EUR][1000 genomes]
rs2693546	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4261830	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4317053	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4346508	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4414801	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4431056	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4602343	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4622858	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4642075	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680411	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680412	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680413	0.99[ASN][1000 genomes]
rs57665991	0.99[ASN][1000 genomes]
rs6441174	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6762706	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6770442	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6773505	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6783175	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6790608	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6794461	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6797626	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6803532	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6803630	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs696715	0.88[EUR][1000 genomes]
rs698975	0.87[EUR][1000 genomes]
rs698976	0.88[EUR][1000 genomes]
rs698977	0.88[EUR][1000 genomes]
rs698979	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs698981	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs698982	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs698983	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs698984	0.86[EUR][1000 genomes]
rs698985	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs698992	0.87[EUR][1000 genomes]
rs699918	0.87[EUR][1000 genomes]
rs699923	0.88[EUR][1000 genomes]
rs699925	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs699926	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7614572	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618071	0.83[EUR][1000 genomes]
rs7622971	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7624303	0.99[ASN][1000 genomes]
rs7630176	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7647342	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653039	0.90[EUR][1000 genomes]
rs827104	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs827130	0.87[EUR][1000 genomes]
rs827139	0.87[EUR][1000 genomes]
rs827141	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs827142	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs827145	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs827146	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs827147	0.86[EUR][1000 genomes]
rs827149	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs827153	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs827155	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs827157	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs827160	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs827162	0.86[EUR][1000 genomes]
rs827168	0.86[EUR][1000 genomes]
rs827170	0.86[EUR][1000 genomes]
rs827173	0.87[EUR][1000 genomes]
rs827174	0.87[EUR][1000 genomes]
rs827801	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs827805	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs844141	0.85[EUR][1000 genomes]
rs860422	0.89[EUR][1000 genomes]
rs862352	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs864331	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs864876	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs866657	0.88[EUR][1000 genomes]
rs9290020	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9290021	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814942	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820954	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848433	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9862337	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9870745	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9871021	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9881063	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883891	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv829768	chr3:157832878-158012070	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6789448	RP11-538P18.2	cis	lung	GTEx
rs6789448	RP11-538P18.2	cis	Artery Tibial	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157828600-157845800	Weak transcription	Spleen	Spleen
2	chr3:157828600-157847800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:157828600-157857000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:157828800-157847600	Weak transcription	NH-A	brain
5	chr3:157828800-157851000	Weak transcription	Right Ventricle	heart
6	chr3:157829000-157849400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:157829200-157841800	Weak transcription	Brain Substantia Nigra	brain
8	chr3:157829200-157842000	Weak transcription	Psoas Muscle	Psoas
9	chr3:157829200-157845400	Weak transcription	HMEC	breast
10	chr3:157829200-157861400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:157830000-157843400	Weak transcription	Small Intestine	intestine
12	chr3:157830000-157866400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:157830200-157841600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:157830400-157845000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:157831800-157845800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:157833200-157856200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:157835400-157845800	Weak transcription	Lung	lung
18	chr3:157835600-157846000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:157835800-157844400	Weak transcription	HUVEC	blood vessel
20	chr3:157836000-157851600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:157836400-157849400	Weak transcription	NHLF	lung
22	chr3:157836600-157841800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:157836600-157842000	Weak transcription	Fetal Brain Male	brain
24	chr3:157836600-157854600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:157836800-157847400	Weak transcription	Colonic Mucosa	Colon
26	chr3:157837000-157843400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:157837400-157841600	Weak transcription	HSMMtube	muscle
28	chr3:157837600-157845800	Weak transcription	Esophagus	oesophagus
29	chr3:157837600-157877600	Weak transcription	Fetal Heart	heart
30	chr3:157838200-157842600	Weak transcription	K562	blood
31	chr3:157838600-157843400	Weak transcription	NHDF-Ad	bronchial
32	chr3:157838800-157841600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:157838800-157862600	Weak transcription	Pancreas	Pancrea
34	chr3:157839000-157842800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:157839200-157841800	Weak transcription	Aorta	Aorta
36	chr3:157839200-157843400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:157839600-157844000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:157839800-157843800	Strong transcription	Dnd41	blood
39	chr3:157839800-157845200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:157839800-157845400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:157839800-157845600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr3:157840000-157841600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:157840000-157842600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:157840000-157850200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:157840200-157841800	Weak transcription	Fetal Brain Female	brain
46	chr3:157840200-157842600	Strong transcription	Colon Smooth Muscle	Colon
47	chr3:157840200-157856000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:157840400-157841800	Strong transcription	Fetal Muscle Leg	muscle
49	chr3:157840400-157844800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:157840600-157842400	Strong transcription	Brain Anterior Caudate	brain

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