Variant report

Variant	rs3130552
Chromosome Location	chr6:31082127-31082128
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	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	chr6:31082102-31082797	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
4	REST	chr6:31081757-31082199	SK-N-SH	brain:	n/a	n/a
5	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
6	REST	chr6:31081568-31082195	PFSK-1	brain:	n/a	chr6:31081698-31081711
7	TCF12	chr6:31082110-31082899	ECC-1	luminal epithelium:	n/a	n/a
8	REST	chr6:31081936-31082148	H1-hESC	embryonic stem cell:	n/a	n/a
9	TCF12	chr6:31081543-31082930	SK-N-SH	brain:	n/a	chr6:31081698-31081708
10	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
11	REST	chr6:31081853-31082253	ECC-1	luminal epithelium:	n/a	n/a
12	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
13	SMARCB1	chr6:31082078-31082664	Hela-S3	cervix:	n/a	chr6:31082449-31082458
14	REST	chr6:31081920-31082178	H1-hESC	embryonic stem cell:	n/a	n/a
15	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
16	PBX3	chr6:31081832-31083025	SK-N-SH	brain:	n/a	n/a
17	NFIC	chr6:31081574-31083228	SK-N-SH	brain:	n/a	n/a
18	TCF12	chr6:31082126-31083212	A549	lung:	n/a	n/a
19	TCF12	chr6:31081554-31082975	SK-N-SH	brain:	n/a	chr6:31081698-31081708
20	TCF12	chr6:31082116-31082897	ECC-1	luminal epithelium:	n/a	n/a
21	RCOR1	chr6:31081316-31083395	IMR90	lung:	n/a	n/a
22	MAX	chr6:31082039-31083196	A549	lung:	n/a	n/a
23	POLR2A	chr6:31082125-31083349	HUVEC	blood vessel:	n/a	n/a
24	FOSL2	chr6:31081716-31082887	SK-N-SH	brain:	n/a	chr6:31082445-31082456 chr6:31082448-31082458 chr6:31081792-31081799 chr6:31082448-31082458 chr6:31082449-31082458 chr6:31082448-31082458 chr6:31082447-31082459 chr6:31082448-31082458
25	MAX	chr6:31082123-31082706	A549	lung:	n/a	n/a

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
ENSG00000204580	Chromatin interaction
ENSG00000204539	Chromatin interaction
ENSG00000137411	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1042126	0.81[AFR][1000 genomes]
rs1042134	0.81[AFR][1000 genomes]
rs1042141	0.81[AFR][1000 genomes]
rs1042145	0.81[AFR][1000 genomes]
rs1042146	0.81[AFR][1000 genomes]
rs1042147	0.81[AFR][1000 genomes]
rs3094215	0.81[AFR][1000 genomes]
rs3094217	0.81[AFR][1000 genomes]
rs3094219	0.81[AFR][1000 genomes]
rs3094220	0.80[ASN][1000 genomes]
rs3095298	0.80[ASN][1000 genomes]
rs3130975	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs3130976	0.80[ASN][1000 genomes]
rs3130977	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130978	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130979	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130982	0.81[AFR][1000 genomes]
rs3130983	0.81[AFR][1000 genomes]
rs3132554	0.81[AFR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3130552	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs3130552	PSORS1C1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31076800-31082200	Weak transcription	Spleen	Spleen
2	chr6:31077600-31082600	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:31078200-31082200	Weak transcription	Gastric	stomach
4	chr6:31078800-31082200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:31078800-31082200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:31079600-31082800	Enhancers	Placenta Amnion	Placenta Amnion
7	chr6:31080000-31082200	Enhancers	HSMMtube	muscle
8	chr6:31080200-31082400	Enhancers	HMEC	breast
9	chr6:31080400-31082200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:31080600-31083800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:31080800-31082200	Enhancers	NHDF-Ad	bronchial
12	chr6:31081000-31083200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr6:31081200-31082200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:31081200-31082200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:31081200-31082200	Enhancers	NH-A	brain
16	chr6:31081200-31082200	Enhancers	NHEK	skin
17	chr6:31081200-31082200	Enhancers	NHLF	lung
18	chr6:31081200-31082400	Enhancers	Right Atrium	heart
19	chr6:31081200-31082600	Enhancers	Adipose Nuclei	Adipose
20	chr6:31081200-31082600	Enhancers	Stomach Mucosa	stomach
21	chr6:31081200-31082800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:31081200-31082800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr6:31081200-31083200	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr6:31081200-31083400	Enhancers	Brain Hippocampus Middle	brain
25	chr6:31081200-31083400	Enhancers	Brain Substantia Nigra	brain
26	chr6:31081200-31085400	Enhancers	Right Ventricle	heart
27	chr6:31081400-31082200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:31081400-31082200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:31081400-31082200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr6:31081400-31082200	Enhancers	Colon Smooth Muscle	Colon
31	chr6:31081400-31082400	Enhancers	Colonic Mucosa	Colon
32	chr6:31081400-31082600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:31081400-31082600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr6:31081400-31083800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:31081600-31082200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr6:31081600-31082200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:31081600-31082200	Enhancers	Esophagus	oesophagus
38	chr6:31081600-31082200	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr6:31081600-31082200	Enhancers	Stomach Smooth Muscle	stomach
40	chr6:31081600-31082200	Enhancers	A549	lung
41	chr6:31081600-31082400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr6:31081600-31082400	Enhancers	Osteobl	bone
43	chr6:31081600-31082600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr6:31081600-31082600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:31081600-31082800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr6:31081600-31082800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:31081600-31082800	Enhancers	Brain Angular Gyrus	brain
48	chr6:31081600-31083000	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr6:31081600-31083200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr6:31081600-31083400	Enhancers	Brain Cingulate Gyrus	brain

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