Variant report

Variant	rs3130554
Chromosome Location	chr6:31082304-31082305
allele	G/T
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	SMARCC1	chr6:31081841-31083341	Hela-S3	cervix:	n/a	chr6:31082449-31082458
2	POLR2A	chr6:31082044-31082957	PFSK-1	brain:	n/a	n/a
3	FOSL2	chr6:31082300-31082778	SK-N-SH	brain:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
4	REST	chr6:31082219-31082725	SK-N-SH	brain:	n/a	chr6:31082466-31082479
5	POLR2A	chr6:31082230-31082609	MCF-7	breast:	n/a	n/a
6	FOS	chr6:31082302-31083000	MCF10A-Er-Src	breast:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082458 chr6:31082447-31082459 chr6:31082448-31082458
7	FOSL2	chr6:31082102-31082797	A549	lung:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
8	FOSL1	chr6:31082011-31083367	HCT-116	colon:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
9	TCF12	chr6:31082110-31082899	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr6:31082158-31082662	MCF-7	breast:	n/a	n/a
11	JUND	chr6:31082259-31082709	A549	lung:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082447-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
12	FOSL2	chr6:31082229-31082710	MCF-7	breast:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
13	FOS	chr6:31082285-31082973	MCF10A-Er-Src	breast:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082458 chr6:31082447-31082459 chr6:31082448-31082458
14	TCF12	chr6:31081543-31082930	SK-N-SH	brain:	n/a	chr6:31081698-31081708
15	FOS	chr6:31082302-31082682	MCF10A-Er-Src	breast:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082458 chr6:31082447-31082459 chr6:31082448-31082458
16	FOS	chr6:31082297-31082843	MCF10A-Er-Src	breast:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082458 chr6:31082447-31082459 chr6:31082448-31082458
17	MAX	chr6:31082148-31082722	SK-N-SH	brain:	n/a	n/a
18	MAX	chr6:31082239-31083001	SK-N-SH	brain:	n/a	n/a
19	JUND	chr6:31081657-31082959	SK-N-SH	brain:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31081792-31081799 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082447-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
20	POLR2A	chr6:31082304-31082513	A549	lung:	n/a	n/a
21	MYC	chr6:31082274-31082363	MCF-7	breast:	n/a	n/a
22	CTCF	chr6:31082260-31082410	GM12869	blood:	n/a	n/a
23	FOSL2	chr6:31082237-31082651	HepG2	liver:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
24	POLR2A	chr6:31082269-31082670	SK-N-SH	brain:	n/a	n/a
25	FOS	chr6:31082084-31082732	HUVEC	blood vessel:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082458 chr6:31082447-31082459 chr6:31082448-31082458
26	POLR2A	chr6:31082218-31082887	SK-N-SH	brain:	n/a	n/a
27	SMARCB1	chr6:31082078-31082664	Hela-S3	cervix:	n/a	chr6:31082449-31082458
28	NFIC	chr6:31082177-31082709	ECC-1	luminal epithelium:	n/a	n/a
29	CHD2	chr6:31082207-31083041	Hela-S3	cervix:	n/a	n/a
30	JUND	chr6:31081759-31082848	SK-N-SH	brain:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31081792-31081799 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082447-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
31	POLR2A	chr6:31082177-31082700	Gliobla	brain:	n/a	n/a
32	PBX3	chr6:31081832-31083025	SK-N-SH	brain:	n/a	n/a
33	NFIC	chr6:31081574-31083228	SK-N-SH	brain:	n/a	n/a
34	TCF7L2	chr6:31082188-31082630	HCT-116	colon:	n/a	chr6:31082449-31082458
35	TCF12	chr6:31082126-31083212	A549	lung:	n/a	n/a
36	GTF2F1	chr6:31082229-31083250	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr6:31082219-31083364	HCT-116	colon:	n/a	n/a
38	TCF12	chr6:31081554-31082975	SK-N-SH	brain:	n/a	chr6:31081698-31081708
39	TCF12	chr6:31082116-31082897	ECC-1	luminal epithelium:	n/a	n/a
40	SP1	chr6:31082220-31083084	A549	lung:	n/a	chr6:31082478-31082492
41	POLR2A	chr6:31082250-31082564	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr6:31082207-31083326	Hela-S3	cervix:	n/a	n/a
43	TCF7L2	chr6:31082280-31082599	Hela-S3	cervix:	n/a	chr6:31082449-31082458
44	NR3C1	chr6:31082229-31082652	A549	lung:	n/a	chr6:31082449-31082458 chr6:31082448-31082457 chr6:31082411-31082418
45	RCOR1	chr6:31081316-31083395	IMR90	lung:	n/a	n/a
46	TAF1	chr6:31082206-31082690	SK-N-SH	brain:	n/a	n/a
47	SP1	chr6:31082243-31083061	A549	lung:	n/a	chr6:31082478-31082492
48	YY1	chr6:31082296-31083081	HCT-116	colon:	n/a	chr6:31082338-31082346 chr6:31082383-31082399 chr6:31082828-31082838
49	POLR2A	chr6:31082246-31082862	HUVEC	blood vessel:	n/a	n/a
50	JUND	chr6:31082274-31083125	Hela-S3	cervix:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082447-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458

No.	Distal block	Cell Line	Cell type
1	chr6:31080693..31083957-chr6:31087484..31089976,3	K562	blood:
2	chr6:30850897..30852602-chr6:31080609..31083224,2	MCF-7	breast:
3	chr6:31079457..31085209-chr6:31085850..31092700,13	MCF-7	breast:
4	chr6:30882036..30883658-chr6:31081525..31084682,3	MCF-7	breast:
5	chr6:31050562..31052756-chr6:31081245..31083912,2	MCF-7	breast:

Variant related genes	Relation type
PSORS1C1	TF binding region
C6orf15	TF binding region
ENSG00000222895	Chromatin interaction
ENSG00000204539	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137411	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1062470	0.82[AFR][1000 genomes]
rs1064190	0.82[EUR][1000 genomes]
rs1064191	0.82[EUR][1000 genomes]
rs1265046	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1265053	0.84[EUR][1000 genomes]
rs1265054	0.83[EUR][1000 genomes]
rs1265055	0.84[EUR][1000 genomes]
rs1265056	0.84[EUR][1000 genomes]
rs1265058	0.84[EUR][1000 genomes]
rs1265059	0.84[EUR][1000 genomes]
rs1265063	0.83[EUR][1000 genomes]
rs1265064	0.84[EUR][1000 genomes]
rs2233966	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2517541	0.81[EUR][1000 genomes]
rs2517556	0.81[EUR][1000 genomes]
rs2535277	0.84[EUR][1000 genomes]
rs2535282	0.81[EUR][1000 genomes]
rs2535283	0.81[EUR][1000 genomes]
rs3091255	0.81[AFR][1000 genomes]
rs3095297	0.82[AFR][1000 genomes]
rs3130553	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3130970	0.80[EUR][1000 genomes]
rs3130980	0.83[AFR][1000 genomes]
rs7381897	0.81[EUR][1000 genomes]
rs9263593	0.81[EUR][1000 genomes]
rs9263597	0.81[EUR][1000 genomes]
rs9263629	0.83[EUR][1000 genomes]
rs9263631	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv462746	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv601489	chr6:31060162-31082361	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	nsv1033227	chr6:31071547-31101674	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv601490	chr6:31079264-31084435	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3130554	HCG22	cis	lymphoblastoid	seeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31077600-31082600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr6:31079600-31082800	Enhancers	Placenta Amnion	Placenta Amnion
3	chr6:31080200-31082400	Enhancers	HMEC	breast
4	chr6:31080600-31083800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:31081000-31083200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
6	chr6:31081200-31082400	Enhancers	Right Atrium	heart
7	chr6:31081200-31082600	Enhancers	Adipose Nuclei	Adipose
8	chr6:31081200-31082600	Enhancers	Stomach Mucosa	stomach
9	chr6:31081200-31082800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:31081200-31082800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr6:31081200-31083200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr6:31081200-31083400	Enhancers	Brain Hippocampus Middle	brain
13	chr6:31081200-31083400	Enhancers	Brain Substantia Nigra	brain
14	chr6:31081200-31085400	Enhancers	Right Ventricle	heart
15	chr6:31081400-31082400	Enhancers	Colonic Mucosa	Colon
16	chr6:31081400-31082600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:31081400-31082600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr6:31081400-31083800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:31081600-31082400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr6:31081600-31082400	Enhancers	Osteobl	bone
21	chr6:31081600-31082600	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr6:31081600-31082600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:31081600-31082800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:31081600-31082800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:31081600-31082800	Enhancers	Brain Angular Gyrus	brain
26	chr6:31081600-31083000	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr6:31081600-31083200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr6:31081600-31083400	Enhancers	Brain Cingulate Gyrus	brain
29	chr6:31081600-31083600	Bivalent Enhancer	Placenta	Placenta
30	chr6:31081600-31084000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:31081600-31085400	Enhancers	Lung	lung
32	chr6:31081800-31082400	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr6:31081800-31082400	Enhancers	HUVEC	blood vessel
34	chr6:31081800-31082800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:31081800-31083200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:31081800-31083200	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr6:31081800-31083200	Enhancers	Fetal Muscle Leg	muscle
38	chr6:31081800-31083200	Bivalent Enhancer	Fetal Stomach	stomach
39	chr6:31081800-31083400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr6:31081800-31083400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:31081800-31083400	Enhancers	Left Ventricle	heart
42	chr6:31081800-31084000	Flanking Active TSS	Hela-S3	cervix
43	chr6:31081800-31085400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:31082000-31082400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:31082000-31082400	Flanking Active TSS	HSMM	muscle
46	chr6:31082000-31082600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
47	chr6:31082000-31082800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr6:31082000-31083000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr6:31082000-31083200	Bivalent Enhancer	HepG2	liver
50	chr6:31082000-31083400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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