Variant report

Variant	rs587712
Chromosome Location	chr3:42631420-42631421
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:42631417-42631428	MCF-7	breast:	n/a	n/a
2	MXI1	chr3:42631206-42633264	SK-N-SH	brain:	n/a	n/a
3	NR2F2	chr3:42631406-42632546	K562	blood:	n/a	n/a
4	POLR2A	chr3:42631332-42633504	HepG2	liver:	n/a	n/a
5	CEBPB	chr3:42631365-42631633	HepG2	liver:	n/a	n/a
6	WRNIP1	chr3:42631326-42631857	GM12878	blood:	n/a	n/a
7	CEBPB	chr3:42631419-42631727	A549	lung:	n/a	n/a
8	CHD1	chr3:42631412-42631835	GM12878	blood:	n/a	n/a
9	CTCF	chr3:42631371-42631439	MCF-7	breast:	n/a	n/a
10	MAX	chr3:42631352-42632576	NB4	blood:	n/a	n/a
11	RFX5	chr3:42631197-42632608	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr3:42631324-42632610	K562	blood:	n/a	n/a
13	POLR2A	chr3:42630896-42632901	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr3:42631203-42632782	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr3:42631268-42631440	K562	blood:	n/a	n/a
16	USF2	chr3:42631317-42631422	Hela-S3	cervix:	n/a	chr3:42631366-42631377
17	JUN	chr3:42630967-42633363	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:42631026..42632613-chr3:42695067..42697159,2	MCF-7	breast:
2	chr3:42629929..42632831-chr3:42695818..42698742,2	MCF-7	breast:
3	chr3:42620803..42625287-chr3:42629964..42635186,7	MCF-7	breast:
4	chr3:42622045..42625365-chr3:42627615..42632564,8	MCF-7	breast:
5	chr3:42629985..42631739-chr3:42857764..42859472,2	MCF-7	breast:
6	chr3:42630327..42632728-chr3:42670152..42672818,2	MCF-7	breast:
7	chr3:42629943..42634676-chr3:42635408..42643782,10	MCF-7	breast:
8	chr3:42617574..42619731-chr3:42628804..42631519,2	MCF-7	breast:

No data

Variant related genes	Relation type
SS18L2	TF binding region
ENSG00000008324	Chromatin interaction
ENSG00000114857	Chromatin interaction
ENSG00000114853	Chromatin interaction
ENSG00000230084	Chromatin interaction
ENSG00000093183	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs2136012	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271181	0.86[EUR][1000 genomes]
rs2271185	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271186	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2976533	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339658	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs339723	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs339725	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs339726	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs339727	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339728	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs339733	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs342521	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs342522	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342536	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs342537	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3774398	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs586082	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597498	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs607568	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612733	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614323	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs617722	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627664	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs638836	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs639692	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640689	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441892	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs663673	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689251	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs704979	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8351	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs925457	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9865109	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs587712	NKTR	cis	Nerve Tibial	GTEx
rs587712	NKTR	cis	Muscle Skeletal	GTEx
rs587712	SEC22C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42624200-42631600	Weak transcription	HSMMtube	muscle
2	chr3:42624400-42632400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:42624800-42631600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:42624800-42631600	Weak transcription	Gastric	stomach
5	chr3:42625000-42631600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:42625200-42631600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:42628800-42631600	Weak transcription	NHLF	lung
8	chr3:42629800-42631600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:42630200-42631600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:42630200-42631800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:42630800-42633000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:42631000-42631600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:42631000-42631600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:42631000-42631600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:42631000-42631600	Enhancers	Esophagus	oesophagus
16	chr3:42631000-42631600	Enhancers	Right Atrium	heart
17	chr3:42631000-42631800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:42631200-42631600	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:42631200-42631600	Enhancers	Primary B cells from peripheral blood	blood
20	chr3:42631200-42631600	Enhancers	Primary T cells from cord blood	blood
21	chr3:42631200-42631600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr3:42631200-42631600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:42631200-42631600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr3:42631200-42631600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr3:42631200-42631600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr3:42631200-42631600	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr3:42631200-42631600	Enhancers	Fetal Lung	lung
28	chr3:42631200-42631600	Enhancers	Fetal Stomach	stomach
29	chr3:42631200-42631600	Enhancers	Pancreas	Pancrea
30	chr3:42631200-42631600	Enhancers	Hela-S3	cervix
31	chr3:42631200-42631800	Flanking Active TSS	GM12878-XiMat	blood
32	chr3:42631200-42631800	Flanking Active TSS	K562	blood
33	chr3:42631200-42632000	Flanking Active TSS	Dnd41	blood
34	chr3:42631400-42631600	Enhancers	H1 Cell Line	embryonic stem cell
35	chr3:42631400-42631600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:42631400-42631600	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr3:42631400-42631600	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr3:42631400-42631600	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr3:42631400-42631600	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr3:42631400-42631600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:42631400-42631600	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr3:42631400-42631600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:42631400-42631600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:42631400-42631600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr3:42631400-42631600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:42631400-42631600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:42631400-42631600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:42631400-42631600	Enhancers	Liver	Liver
49	chr3:42631400-42631600	Flanking Active TSS	Brain Hippocampus Middle	brain
50	chr3:42631400-42631600	Enhancers	Brain Substantia Nigra	brain

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