Variant report

Variant	rs7739241
Chromosome Location	chr6:86575796-86575797
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:86575630-86575801	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr6:86575752-86576114	MCF10A-Er-Src	breast:	n/a	chr6:86575918-86575929
3	FOSL2	chr6:86575738-86576068	HepG2	liver:	n/a	chr6:86575919-86575930
4	JUN	chr6:86575739-86576236	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr6:86575723-86575841	HUVEC	blood vessel:	n/a	n/a
6	FOS	chr6:86575787-86576081	MCF10A-Er-Src	breast:	n/a	chr6:86575918-86575929
7	FOSL2	chr6:86575711-86576162	HepG2	liver:	n/a	chr6:86575919-86575930
8	JUND	chr6:86575749-86576093	HepG2	liver:	n/a	n/a
9	NR3C1	chr6:86575716-86576097	ECC-1	luminal epithelium:	n/a	n/a
10	FOS	chr6:86575752-86576396	HUVEC	blood vessel:	n/a	chr6:86575918-86575929
11	IRF1	chr6:86575677-86575993	K562	blood:	n/a	n/a
12	JUND	chr6:86575788-86576054	HepG2	liver:	n/a	n/a
13	PRDM1	chr6:86575661-86576038	Hela-S3	cervix:	n/a	chr6:86575837-86575852
14	IRF1	chr6:86575668-86576056	K562	blood:	n/a	n/a
15	FOS	chr6:86575755-86576114	MCF10A-Er-Src	breast:	n/a	chr6:86575918-86575929
16	NFIC	chr6:86575583-86576159	ECC-1	luminal epithelium:	n/a	n/a
17	TEAD4	chr6:86575700-86576177	HepG2	liver:	n/a	n/a
18	FOXA2	chr6:86575770-86576049	HepG2	liver:	n/a	n/a
19	MAFK	chr6:86575741-86575924	IMR90	lung:	n/a	n/a
20	FOXA1	chr6:86575758-86576071	HepG2	liver:	n/a	n/a
21	FOS	chr6:86575770-86576113	MCF10A-Er-Src	breast:	n/a	chr6:86575918-86575929
22	NR3C1	chr6:86575780-86576110	ECC-1	luminal epithelium:	n/a	n/a
23	NFIC	chr6:86575614-86576275	ECC-1	luminal epithelium:	n/a	n/a
24	TEAD4	chr6:86575729-86576168	ECC-1	luminal epithelium:	n/a	n/a
25	E2F4	chr6:86575794-86575947	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86386983..86389313-chr6:86573645..86576019,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000218766	TF binding region
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1059306	0.82[CEU][hapmap]
rs10944136	0.83[ASN][1000 genomes]
rs10944137	1.00[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap]
rs10944144	0.90[EUR][1000 genomes]
rs10944145	0.90[EUR][1000 genomes]
rs10944147	0.91[EUR][1000 genomes]
rs10944151	0.89[EUR][1000 genomes]
rs10944152	0.90[EUR][1000 genomes]
rs10944157	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1173417	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs11752180	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11752223	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11755642	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap]
rs11758508	1.00[CEU][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs12153887	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12190603	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs12191212	0.90[EUR][1000 genomes]
rs12192546	1.00[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap]
rs12193904	1.00[CEU][hapmap]
rs12196377	0.94[EUR][1000 genomes]
rs12198061	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12198557	0.85[EUR][1000 genomes]
rs12198730	0.91[EUR][1000 genomes]
rs12199329	0.90[EUR][1000 genomes]
rs12201741	0.82[EUR][1000 genomes]
rs12202712	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209668	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12211216	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12212480	1.00[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap]
rs12215159	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12660846	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12664634	0.82[ASN][1000 genomes]
rs12665464	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12665516	0.90[EUR][1000 genomes]
rs12665542	0.90[EUR][1000 genomes]
rs13192974	0.81[ASN][1000 genomes]
rs13199006	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13200064	0.80[EUR][1000 genomes]
rs13201730	0.91[EUR][1000 genomes]
rs13203309	0.89[EUR][1000 genomes]
rs13203560	0.91[EUR][1000 genomes]
rs13207173	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs13207537	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13209671	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13209740	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13213603	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13214489	0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13219504	0.91[EUR][1000 genomes]
rs1335442	1.00[CEU][hapmap];0.90[GIH][hapmap];0.97[TSI][hapmap]
rs1447160	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1470531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1813001	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1838954	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1838955	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1838958	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1838959	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1995688	0.90[CEU][hapmap]
rs2084293	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2084294	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2084296	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2084297	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2100109	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2121594	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2166665	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2197648	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2218594	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2225754	1.00[CEU][hapmap]
rs2324817	0.81[ASN][1000 genomes]
rs2475792	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs2783171	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs2875456	0.82[EUR][1000 genomes]
rs34795473	0.81[ASN][1000 genomes]
rs35874630	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36035797	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36053156	0.97[EUR][1000 genomes]
rs4098044	0.81[ASN][1000 genomes]
rs4706246	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4706248	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4706252	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4706253	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4706254	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4707223	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4707229	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4707236	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4707239	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57016132	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61119084	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6454487	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.80[ASN][1000 genomes]
rs6454488	0.81[ASN][1000 genomes]
rs6454504	0.82[ASN][1000 genomes]
rs66807489	0.80[ASN][1000 genomes]
rs67024565	0.91[EUR][1000 genomes]
rs6900436	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6914463	0.80[AFR][1000 genomes]
rs7742201	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs7755730	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7766645	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9344542	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs9353327	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs9647601	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028293	chr6:86353958-86778912	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases
2	nsv538350	chr6:86353958-86778912	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases
3	nsv886335	chr6:86445651-86669361	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1022618	chr6:86465365-87432069	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv538352	chr6:86465365-87432069	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1033637	chr6:86482045-86701733	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538353	chr6:86482045-86701733	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv526067	chr6:86538718-86576854	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1802672	chr6:86546123-86662267	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv522858	chr6:86550985-86578833	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1018453	chr6:86555984-86761120	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	esv3451810	chr6:86564474-86577360	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs7739241	SNHG5	cis	Adipose Subcutaneous	GTEx
rs7739241	SNHG5	cis	Artery Tibial	GTEx
rs7739241	SNHG5	cis	Artery Aorta	GTEx
rs7739241	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs7739241	SNHG5	cis	Nerve Tibial	GTEx
rs7739241	C6orf160	cis	uninvolved skin	skin_eQTL
rs7739241	SNHG5	cis	multi-tissue	Pritchard
rs7739241	SNHG5	cis	lung	GTEx
rs7739241	SNHG5	cis	Muscle Skeletal	GTEx
rs7739241	SNHG5	cis	Esophagus Mucosa	GTEx
rs7739241	SNHG5	cis	lymphoblastoid	seeQTL
rs7739241	SNHG5	cis	Heart Left Ventricle	GTEx
rs7739241	C6orf160	cis	lesional skin	skin_eQTL
rs7739241	SNHG5	cis	Thyroid	GTEx
rs7739241	SNHG5	cis	Esophagus Muscularis	GTEx
rs7739241	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs7739241	SNHG5	cis	Whole Blood	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86563200-86577800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:86568200-86576800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:86574400-86576400	Active TSS	NHDF-Ad	bronchial
4	chr6:86574600-86576000	Enhancers	Fetal Heart	heart
5	chr6:86574600-86576200	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr6:86574600-86576200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:86574600-86576200	Active TSS	Brain Angular Gyrus	brain
8	chr6:86574600-86576600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr6:86574800-86575800	Enhancers	Fetal Brain Male	brain
10	chr6:86574800-86576200	Active TSS	Aorta	Aorta
11	chr6:86574800-86576200	Flanking Active TSS	HUVEC	blood vessel
12	chr6:86575000-86575800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:86575000-86575800	Enhancers	Spleen	Spleen
14	chr6:86575000-86576200	Flanking Active TSS	Dnd41	blood
15	chr6:86575000-86576400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:86575000-86576400	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr6:86575000-86576600	Active TSS	Colonic Mucosa	Colon
18	chr6:86575000-86576600	Enhancers	Lung	lung
19	chr6:86575000-86576600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr6:86575000-86577000	Enhancers	H1 Cell Line	embryonic stem cell
21	chr6:86575200-86575800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:86575200-86575800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
23	chr6:86575200-86576000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr6:86575200-86576000	Active TSS	Primary hematopoietic stem cells	blood
25	chr6:86575200-86576000	Active TSS	Monocytes-CD14+_RO01746	blood
26	chr6:86575200-86576200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:86575200-86576200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:86575200-86576200	Active TSS	Rectal Smooth Muscle	rectum
29	chr6:86575200-86576400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr6:86575200-86576400	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr6:86575200-86576400	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr6:86575200-86576600	Active TSS	Brain Substantia Nigra	brain
33	chr6:86575200-86576600	Active TSS	NHLF	lung
34	chr6:86575200-86576800	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr6:86575200-86577200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr6:86575200-86583400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:86575400-86575800	Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr6:86575400-86575800	Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr6:86575400-86575800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:86575400-86575800	Active TSS	Gastric	stomach
41	chr6:86575400-86576000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:86575400-86576000	Active TSS	Primary T cells fromperipheralblood	blood
43	chr6:86575400-86576000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:86575400-86576000	Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr6:86575400-86576000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr6:86575400-86576000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr6:86575400-86576000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:86575400-86576000	Active TSS	Liver	Liver
49	chr6:86575400-86576000	Active TSS	Brain Cingulate Gyrus	brain
50	chr6:86575400-86576000	Active TSS	Brain Inferior Temporal Lobe	brain

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