Variant report

Variant	rs1042147
Chromosome Location	chr6:31083156-31083157
allele	C/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	RAD21	chr6:31082699-31083229	A549	lung:	n/a	n/a
3	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
4	CTCF	chr6:31083040-31083190	HFF-Myc	foreskin:	n/a	n/a
5	RAD21	chr6:31082359-31083165	Hela-S3	cervix:	n/a	chr6:31082419-31082433
6	SMC3	chr6:31082344-31083304	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr6:31082449-31083233	Hela-S3	cervix:	n/a	n/a
8	RAD21	chr6:31082738-31083228	MCF-7	breast:	n/a	n/a
9	POLR2A	chr6:31083056-31083221	MCF-7	breast:	n/a	n/a
10	CTCF	chr6:31082652-31083345	A549	lung:	n/a	n/a
11	CTCF	chr6:31082722-31083245	K562	blood:	n/a	n/a
12	CTCF	chr6:31083040-31083190	A549	lung:	n/a	n/a
13	NFIC	chr6:31081574-31083228	SK-N-SH	brain:	n/a	n/a
14	CTCF	chr6:31082812-31083164	IMR90	lung:	n/a	n/a
15	TCF12	chr6:31082126-31083212	A549	lung:	n/a	n/a
16	GTF2F1	chr6:31082229-31083250	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr6:31082219-31083364	HCT-116	colon:	n/a	n/a
18	CTCF	chr6:31083060-31083210	HFF-Myc	foreskin:	n/a	n/a
19	ZKSCAN1	chr6:31082390-31083207	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr6:31083014-31083277	MCF-7	breast:	n/a	n/a
21	POLR2A	chr6:31082999-31083242	Gliobla	brain:	n/a	n/a
22	POLR2A	chr6:31082207-31083326	Hela-S3	cervix:	n/a	n/a
23	RCOR1	chr6:31081316-31083395	IMR90	lung:	n/a	n/a
24	RAD21	chr6:31082790-31083162	H1-hESC	embryonic stem cell:	n/a	n/a
25	RAD21	chr6:31082733-31083186	SK-N-SH_RA	brain:	n/a	n/a
26	POLR2A	chr6:31082189-31083404	Hela-S3	cervix:	n/a	n/a
27	MAX	chr6:31082039-31083196	A549	lung:	n/a	n/a
28	POLR2A	chr6:31082125-31083349	HUVEC	blood vessel:	n/a	n/a
29	RAD21	chr6:31082666-31083234	A549	lung:	n/a	n/a
30	POLR2A	chr6:31082266-31083287	HCT-116	colon:	n/a	n/a
31	CTCF	chr6:31083154-31083170	NHEK	skin:	n/a	n/a
32	POLR2A	chr6:31082302-31083273	Hela-S3	cervix:	n/a	n/a
33	RCOR1	chr6:31082328-31083226	Hela-S3	cervix:	n/a	n/a

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	chr6:30850897..30852602-chr6:31080609..31083224,2	MCF-7	breast:
4	chr6:31079457..31085209-chr6:31085850..31092700,13	MCF-7	breast:
5	chr6:30882036..30883658-chr6:31081525..31084682,3	MCF-7	breast:
6	chr6:31050562..31052756-chr6:31081245..31083912,2	MCF-7	breast:
7	chr6:31082945..31085753-chr6:31086345..31088520,3	MCF-7	breast:

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

Extended variants
information (count: 30 )
Associated
traits (count: 26 )

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]
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:26)

SNP	Gene	Cis/trans	Tissue	Source
rs1042147	PSORS1C1	cis	Adipose Subcutaneous	GTEx
rs1042147	PSORS1C2	cis	Artery Tibial	GTEx
rs1042147	XXbac-BPG248L24.12	cis	Whole Blood	GTEx
rs1042147	PSORS1C1	cis	Skin Sun Exposed Lower leg	GTEx
rs1042147	PSORS1C2	cis	Nerve Tibial	GTEx
rs1042147	ANKS1A	cis	cerebellum	SCAN
rs1042147	PSORS1C1	cis	Esophagus Muscularis	GTEx
rs1042147	PSORS1C2	cis	Esophagus Muscularis	GTEx
rs1042147	CCHCR1	Cis_1M	lymphoblastoid	RTeQTL
rs1042147	PSORS1C2	cis	Stomach	GTEx
rs1042147	PSORS1C1	cis	Artery Aorta	GTEx
rs1042147	PSORS1C1	cis	normal skin	skin_eQTL
rs1042147	PSORS1C1	cis	Artery Tibial	GTEx
rs1042147	CCHCR1	cis	lymphoblastoid	seeQTL
rs1042147	PSORS1C2	cis	Artery Aorta	GTEx
rs1042147	PSORS1C2	cis	Esophagus Mucosa	GTEx
rs1042147	PSORS1C2	cis	lung	GTEx
rs1042147	PSORS1C1	cis	Esophagus Mucosa	GTEx
rs1042147	PSORS1C1	cis	Thyroid	GTEx
rs1042147	PSORS1C1	cis	Heart Left Ventricle	GTEx
rs1042147	PSORS1C1	cis	Nerve Tibial	GTEx
rs1042147	HMGA1	cis	cerebellum	SCAN
rs1042147	PSORS1C1	cis	Stomach	GTEx
rs1042147	PSORS1C1	cis	lung	GTEx
rs1042147	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs1042147	PSORS1C2	cis	Thyroid	GTEx

Chromatin state (count:84 , 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	chr6:31081000-31083200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
3	chr6:31081200-31083200	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr6:31081200-31083400	Enhancers	Brain Hippocampus Middle	brain
5	chr6:31081200-31083400	Enhancers	Brain Substantia Nigra	brain
6	chr6:31081200-31085400	Enhancers	Right Ventricle	heart
7	chr6:31081400-31083800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:31081600-31083200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr6:31081600-31083400	Enhancers	Brain Cingulate Gyrus	brain
10	chr6:31081600-31083600	Bivalent Enhancer	Placenta	Placenta
11	chr6:31081600-31084000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:31081600-31085400	Enhancers	Lung	lung
13	chr6:31081800-31083200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:31081800-31083200	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr6:31081800-31083200	Enhancers	Fetal Muscle Leg	muscle
16	chr6:31081800-31083200	Bivalent Enhancer	Fetal Stomach	stomach
17	chr6:31081800-31083400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr6:31081800-31083400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:31081800-31083400	Enhancers	Left Ventricle	heart
20	chr6:31081800-31084000	Flanking Active TSS	Hela-S3	cervix
21	chr6:31081800-31085400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:31082000-31083200	Bivalent Enhancer	HepG2	liver
23	chr6:31082000-31083400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:31082000-31083600	Enhancers	Ovary	ovary
25	chr6:31082200-31083200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:31082200-31083200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr6:31082200-31083200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr6:31082200-31083200	Enhancers	Brain Anterior Caudate	brain
29	chr6:31082200-31083200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr6:31082200-31083200	Enhancers	Spleen	Spleen
31	chr6:31082200-31083400	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr6:31082200-31083400	Enhancers	Small Intestine	intestine
33	chr6:31082200-31083400	Flanking Active TSS	Stomach Smooth Muscle	stomach
34	chr6:31082200-31083600	Flanking Active TSS	NHEK	skin
35	chr6:31082200-31083800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:31082200-31083800	Flanking Active TSS	Rectal Smooth Muscle	rectum
37	chr6:31082200-31084000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:31082200-31084400	Enhancers	Gastric	stomach
39	chr6:31082400-31083200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:31082400-31083200	Flanking Active TSS	Colonic Mucosa	Colon
41	chr6:31082400-31083200	Enhancers	Fetal Muscle Trunk	muscle
42	chr6:31082400-31083200	Active TSS	A549	lung
43	chr6:31082400-31083400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr6:31082400-31083400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:31082400-31083600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:31082400-31083600	Flanking Active TSS	HUVEC	blood vessel
47	chr6:31082400-31083600	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr6:31082400-31084000	Flanking Active TSS	HMEC	breast
49	chr6:31082600-31083200	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr6:31082600-31083200	Flanking Active TSS	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links