Variant report

Variant	rs1042145
Chromosome Location	chr6:31083328-31083329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

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	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
3	CTCF	chr6:31082652-31083345	A549	lung:	n/a	n/a
4	POLR2A	chr6:31082219-31083364	HCT-116	colon:	n/a	n/a
5	RCOR1	chr6:31081316-31083395	IMR90	lung:	n/a	n/a
6	POLR2A	chr6:31082189-31083404	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr6:31082125-31083349	HUVEC	blood vessel:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:31083322-31083372	MCF10A-Er-Src	breast:	n/a
2	chr6:31083322-31083372	HUVEC	blood vessel:	n/a
3	chr6:31083322-31083372	H1-hESC	embryonic stem cell:	embryo
4	chr6:31083322-31083372	CMK	blood:	n/a
5	chr6:31083322-31083372	NB4	blood:	n/a
6	chr6:31083322-31083372	Hela-S3	cervix:	n/a
7	chr6:31083322-31083372	GM12892	blood:	n/a
8	chr6:31083322-31083372	HRPEpiC	eye:	n/a
9	chr6:31083322-31083372	HCF	heart:	n/a
10	chr6:31083322-31083372	HCPEpiC	choroid plexus:	n/a
11	chr6:31083322-31083372	NH-A	brain:	n/a
12	chr6:31083322-31083372	NHBE	bronchial:	n/a
13	chr6:31083322-31083372	NT2-D1	testis:	n/a
14	chr6:31083322-31083372	AG09309	skin:	n/a
15	chr6:31083322-31083372	HCM	heart:	n/a
16	chr6:31083322-31083372	GM12878	blood:	n/a
17	chr6:31083322-31083372	NHDF-neo	bronchial:	n/a
18	chr6:31083322-31083372	AG10803	skin:	n/a
19	chr6:31083322-31083372	Caco-2	colon:	n/a
20	chr6:31083322-31083372	U87	brain:	n/a
21	chr6:31083322-31083372	ProgFib	skin:	n/a
22	chr6:31083322-31083372	BJ	skin:	n/a
23	chr6:31083322-31083372	MCF-7	breast:	n/a
24	chr6:31083322-31083372	AG09319	gingival:	n/a
25	chr6:31083322-31083372	ovcar-3	ovarian:	n/a
26	chr6:31083322-31083372	ECC-1	luminal epithelium:	n/a
27	chr6:31083322-31083372	HEK293	kidney:	embryo
28	chr6:31083322-31083372	PANC-1	pancreas:	n/a
29	chr6:31083322-31083372	HRCEpiC	kidney:	n/a
30	chr6:31083322-31083372	BE2_C	brain:	n/a
31	chr6:31083322-31083372	HCT-116	colon:	n/a
32	chr6:31083322-31083372	SKMC	muscle:	n/a
33	chr6:31083322-31083372	LNCaP	prostate:	n/a
34	chr6:31083322-31083372	PFSK-1	brain:	n/a
35	chr6:31083322-31083372	HAEpiC	amniotic membrane:	n/a
36	chr6:31083322-31083372	HEEpiC	esophagus:	n/a
37	chr6:31083322-31083372	AG04450	lung:	fetal
38	chr6:31083322-31083372	HL-60	blood:	n/a
39	chr6:31083322-31083372	Jurkat	blood:	n/a
40	chr6:31083322-31083372	HNPCEpiC	eye:	n/a
41	chr6:31083322-31083372	GM12891	blood:	n/a
42	chr6:31083322-31083372	HepG2	liver:	n/a
43	chr6:31083322-31083372	HRE	kidney:	n/a
44	chr6:31083322-31083372	A549	lung:	n/a
45	chr6:31083322-31083372	HPAEpiC	pulmonary alveolar:	n/a
46	chr6:31083322-31083372	K562	blood:	n/a
47	chr6:31083322-31083372	PrEC	prostate:	n/a
48	chr6:31083322-31083372	Hepatocyte	liver:	n/a
49	chr6:31083322-31083372	IMR90	lung:	fetal
50	chr6:31083322-31083372	SK-N-MC	brain:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31080693..31083957-chr6:31087484..31089976,3	K562	blood:
2	chr6:30852881..30854431-chr6:31082824..31085360,2	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:
6	chr6:31082945..31085753-chr6:31086345..31088520,3	MCF-7	breast:

No data

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

Extended variants
information (count: 30 )
Associated
traits (count: 22 )

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]
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]
rs3130983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:16 , 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	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
13	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
14	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
15	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
16	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

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs1042145	PSORS1C1	cis	Artery Aorta	GTEx
rs1042145	PSORS1C1	cis	Skin Sun Exposed Lower leg	GTEx
rs1042145	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs1042145	PSORS1C2	cis	Artery Aorta	GTEx
rs1042145	PSORS1C1	cis	Adipose Subcutaneous	GTEx
rs1042145	PSORS1C2	cis	Nerve Tibial	GTEx
rs1042145	PSORS1C2	cis	Esophagus Muscularis	GTEx
rs1042145	PSORS1C2	cis	Artery Tibial	GTEx
rs1042145	PSORS1C1	cis	Thyroid	GTEx
rs1042145	PSORS1C1	cis	Artery Tibial	GTEx
rs1042145	PSORS1C2	cis	Stomach	GTEx
rs1042145	PSORS1C1	cis	Esophagus Mucosa	GTEx
rs1042145	CCHCR1	Cis_1M	lymphoblastoid	RTeQTL
rs1042145	PSORS1C2	cis	Thyroid	GTEx
rs1042145	PSORS1C1	cis	Stomach	GTEx
rs1042145	XXbac-BPG248L24.12	cis	Whole Blood	GTEx
rs1042145	PSORS1C1	cis	Nerve Tibial	GTEx
rs1042145	PSORS1C1	cis	lung	GTEx
rs1042145	PSORS1C1	cis	Heart Left Ventricle	GTEx
rs1042145	PSORS1C1	cis	Esophagus Muscularis	GTEx
rs1042145	PSORS1C2	cis	Esophagus Mucosa	GTEx
rs1042145	PSORS1C2	cis	lung	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31080600-31083800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:31081200-31083400	Enhancers	Brain Hippocampus Middle	brain
3	chr6:31081200-31083400	Enhancers	Brain Substantia Nigra	brain
4	chr6:31081200-31085400	Enhancers	Right Ventricle	heart
5	chr6:31081400-31083800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:31081600-31083400	Enhancers	Brain Cingulate Gyrus	brain
7	chr6:31081600-31083600	Bivalent Enhancer	Placenta	Placenta
8	chr6:31081600-31084000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:31081600-31085400	Enhancers	Lung	lung
10	chr6:31081800-31083400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr6:31081800-31083400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:31081800-31083400	Enhancers	Left Ventricle	heart
13	chr6:31081800-31084000	Flanking Active TSS	Hela-S3	cervix
14	chr6:31081800-31085400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:31082000-31083400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:31082000-31083600	Enhancers	Ovary	ovary
17	chr6:31082200-31083400	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr6:31082200-31083400	Enhancers	Small Intestine	intestine
19	chr6:31082200-31083400	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr6:31082200-31083600	Flanking Active TSS	NHEK	skin
21	chr6:31082200-31083800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:31082200-31083800	Flanking Active TSS	Rectal Smooth Muscle	rectum
23	chr6:31082200-31084000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:31082200-31084400	Enhancers	Gastric	stomach
25	chr6:31082400-31083400	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr6:31082400-31083400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:31082400-31083600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:31082400-31083600	Flanking Active TSS	HUVEC	blood vessel
29	chr6:31082400-31083600	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr6:31082400-31084000	Flanking Active TSS	HMEC	breast
31	chr6:31082600-31083400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:31082600-31083400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr6:31082600-31083400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:31082600-31083400	Flanking Active TSS	NH-A	brain
35	chr6:31082600-31083600	Flanking Active TSS	Stomach Mucosa	stomach
36	chr6:31082600-31092800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:31082800-31083400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:31082800-31083400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:31082800-31083400	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr6:31082800-31083600	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr6:31082800-31083600	Flanking Active TSS	Colon Smooth Muscle	Colon
42	chr6:31082800-31083600	Bivalent Enhancer	GM12878-XiMat	blood
43	chr6:31082800-31084000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:31082800-31085000	Weak transcription	Brain Angular Gyrus	brain
45	chr6:31082800-31093000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:31083000-31083400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr6:31083000-31083400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr6:31083000-31083400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr6:31083000-31083400	Enhancers	NHLF	lung
50	chr6:31083000-31083400	Enhancers	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links