Variant report

Variant	rs3130983
Chromosome Location	chr6:31084792-31084793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr6:31084791-31085172	PFSK-1	brain:	n/a	n/a
2	REST	chr6:31084775-31085158	PFSK-1	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30852881..30854431-chr6:31082824..31085360,2	MCF-7	breast:
2	chr6:30706968..30708550-chr6:31084295..31086669,2	MCF-7	breast:
3	chr6:31079457..31085209-chr6:31085850..31092700,13	MCF-7	breast:
4	chr6:31081417..31083958-chr6:31084326..31085918,2	K562	blood:
5	chr6:31082945..31085753-chr6:31086345..31088520,3	MCF-7	breast:

No data

Variant related genes	Relation type
C6orf15	TF binding region
ENSG00000204540	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000204539	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1042126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1042134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1042141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1042145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1042146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1042147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094218	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130552	0.81[AFR][1000 genomes]
rs3130979	0.82[AFR][1000 genomes]
rs3130982	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
12	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
13	nsv462747	chr6:31082361-31092124	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv601491	chr6:31082361-31092124	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv884137	chr6:31082361-31129310	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers 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	22 gene(s)	inside rSNPs	diseases
16	esv1797052	chr6:31083813-31095816	Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	esv1820685	chr6:31083813-31097453	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs3130983	PSORS1C2	cis	Esophagus Muscularis	GTEx
rs3130983	PSORS1C1	cis	Esophagus Muscularis	GTEx
rs3130983	PSORS1C2	cis	Artery Tibial	GTEx
rs3130983	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs3130983	PSORS1C2	cis	Esophagus Mucosa	GTEx
rs3130983	PSORS1C1	cis	lung	GTEx
rs3130983	PSORS1C2	cis	Thyroid	GTEx
rs3130983	PSORS1C1	cis	Esophagus Mucosa	GTEx
rs3130983	PSORS1C1	cis	Artery Aorta	GTEx
rs3130983	PSORS1C1	cis	Heart Left Ventricle	GTEx
rs3130983	PSORS1C1	cis	Stomach	GTEx
rs3130983	PSORS1C2	cis	lung	GTEx
rs3130983	XXbac-BPG248L24.12	cis	Whole Blood	GTEx
rs3130983	PSORS1C1	cis	Thyroid	GTEx
rs3130983	ANKS1A	cis	cerebellum	SCAN
rs3130983	PSORS1C2	cis	Artery Aorta	GTEx
rs3130983	PSORS1C2	cis	Nerve Tibial	GTEx
rs3130983	PSORS1C1	cis	Nerve Tibial	GTEx
rs3130983	CCHCR1	Cis_1M	lymphoblastoid	RTeQTL
rs3130983	CCHCR1	cis	lymphoblastoid	seeQTL
rs3130983	PSORS1C1	cis	Skin Sun Exposed Lower leg	GTEx
rs3130983	PSORS1C1	cis	Adipose Subcutaneous	GTEx
rs3130983	HMGA1	cis	cerebellum	SCAN
rs3130983	PSORS1C2	cis	Stomach	GTEx
rs3130983	PSORS1C1	cis	Artery Tibial	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31081200-31085400	Enhancers	Right Ventricle	heart
2	chr6:31081600-31085400	Enhancers	Lung	lung
3	chr6:31081800-31085400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:31082600-31092800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:31082800-31085000	Weak transcription	Brain Angular Gyrus	brain
6	chr6:31082800-31093000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:31083200-31084800	Enhancers	Adipose Nuclei	Adipose
8	chr6:31083200-31085400	Enhancers	Esophagus	oesophagus
9	chr6:31083200-31085600	Enhancers	Right Atrium	heart
10	chr6:31083200-31092800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:31083200-31094200	Weak transcription	Aorta	Aorta
12	chr6:31083200-31105400	Weak transcription	Spleen	Spleen
13	chr6:31083400-31084800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:31083400-31084800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:31083400-31084800	Weak transcription	Brain Substantia Nigra	brain
16	chr6:31083400-31085200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:31083400-31087800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:31083400-31090000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:31083400-31093400	Weak transcription	HSMMtube	muscle
20	chr6:31083600-31084800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:31083600-31085000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:31083600-31085000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr6:31083600-31085400	Enhancers	Colon Smooth Muscle	Colon
24	chr6:31083600-31085400	Enhancers	Stomach Mucosa	stomach
25	chr6:31083600-31085400	Transcr. at gene 5' and 3'	NHEK	skin
26	chr6:31083600-31091000	Weak transcription	A549	lung
27	chr6:31083600-31092600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:31083800-31085000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr6:31083800-31085000	Enhancers	Rectal Smooth Muscle	rectum
30	chr6:31083800-31085400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:31083800-31089600	Weak transcription	HUVEC	blood vessel
32	chr6:31083800-31090000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:31083800-31090200	Weak transcription	HSMM	muscle
34	chr6:31083800-31093600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:31084000-31085400	Enhancers	Ovary	ovary
36	chr6:31084000-31086600	Enhancers	Placenta Amnion	Placenta Amnion
37	chr6:31084200-31086200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:31084400-31084800	Enhancers	Left Ventricle	heart
39	chr6:31084400-31085000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:31084400-31085200	Bivalent Enhancer	Placenta	Placenta
41	chr6:31084400-31085400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr6:31084400-31089200	Weak transcription	Gastric	stomach
43	chr6:31084600-31084800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr6:31084600-31084800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:31084600-31084800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:31084600-31084800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:31084600-31084800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:31084600-31084800	Enhancers	Colonic Mucosa	Colon
49	chr6:31084600-31085000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:31084600-31085000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin

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