Variant report

Variant	rs1062470
Chromosome Location	chr6:31084435-31084436
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr6:30882036..30883658-chr6:31081525..31084682,3	MCF-7	breast:
6	chr6:31082945..31085753-chr6:31086345..31088520,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204539	Chromatin interaction
ENSG00000204540	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000204580	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs2239522	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3091255	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130553	0.80[AFR][1000 genomes]
rs3130554	0.82[AFR][1000 genomes]
rs3130980	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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
17	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
18	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1062470	PSORS1C1	cis	Esophagus Mucosa	GTEx
rs1062470	CCHCR1	Cis_1M	lymphoblastoid	RTeQTL
rs1062470	CCHCR1	cis	lymphoblastoid	seeQTL
rs1062470	PSORS1C2	cis	Esophagus Mucosa	GTEx
rs1062470	XXbac-BPG248L24.12	cis	Thyroid	GTEx
rs1062470	XXbac-BPG248L24.12	cis	Whole Blood	GTEx
rs1062470	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs1062470	HLA-DRB5	cis	cerebellum	SCAN

Chromatin state (count:54 , 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	chr6:31083200-31084600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:31083200-31084800	Enhancers	Adipose Nuclei	Adipose
9	chr6:31083200-31085400	Enhancers	Esophagus	oesophagus
10	chr6:31083200-31085600	Enhancers	Right Atrium	heart
11	chr6:31083200-31092800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:31083200-31094200	Weak transcription	Aorta	Aorta
13	chr6:31083200-31105400	Weak transcription	Spleen	Spleen
14	chr6:31083400-31084600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:31083400-31084600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:31083400-31084600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:31083400-31084600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:31083400-31084600	Weak transcription	Pancreas	Pancrea
19	chr6:31083400-31084800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:31083400-31084800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr6:31083400-31084800	Weak transcription	Brain Substantia Nigra	brain
22	chr6:31083400-31085200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr6:31083400-31087800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:31083400-31090000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr6:31083400-31093400	Weak transcription	HSMMtube	muscle
26	chr6:31083600-31084800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:31083600-31085000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr6:31083600-31085000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:31083600-31085400	Enhancers	Colon Smooth Muscle	Colon
30	chr6:31083600-31085400	Enhancers	Stomach Mucosa	stomach
31	chr6:31083600-31085400	Transcr. at gene 5' and 3'	NHEK	skin
32	chr6:31083600-31091000	Weak transcription	A549	lung
33	chr6:31083600-31092600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:31083800-31084600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:31083800-31084600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:31083800-31085000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr6:31083800-31085000	Enhancers	Rectal Smooth Muscle	rectum
38	chr6:31083800-31085400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:31083800-31089600	Weak transcription	HUVEC	blood vessel
40	chr6:31083800-31090000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr6:31083800-31090200	Weak transcription	HSMM	muscle
42	chr6:31083800-31093600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:31084000-31084600	Enhancers	HMEC	breast
44	chr6:31084000-31085400	Enhancers	Ovary	ovary
45	chr6:31084000-31086600	Enhancers	Placenta Amnion	Placenta Amnion
46	chr6:31084200-31086200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:31084400-31084600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:31084400-31084600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr6:31084400-31084600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr6:31084400-31084800	Enhancers	Left Ventricle	heart

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