Variant report

Variant	rs9501057
Chromosome Location	chr6:31106516-31106517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:31103022..31109591-chr6:31125707..31129394,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSORS1C1-1	chr6:31106136-31107219	NONHSAT108723

Variant related genes	Relation type
ENSG00000137310	Chromatin interaction
ENSG00000204536	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11965454	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11967883	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs130074	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16898844	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17190839	0.88[ASN][1000 genomes]
rs17197199	0.88[ASN][1000 genomes]
rs2072108	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2073716	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2073718	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240061	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2285804	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59044818	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60483630	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62398818	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6901657	0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9500876	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9501058	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9501062	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9501063	0.81[EUR][1000 genomes];0.91[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	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
12	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
13	esv33699	chr6:31094845-31110011	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv1019637	chr6:31104401-31354706	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
15	nsv1029569	chr6:31104401-31412740	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
16	nsv538174	chr6:31104401-31412740	Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9501057	CCHCR1	cis	multi-tissue	Pritchard
rs9501057	CCHCR1	cis	lymphoblastoid	seeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31093400-31107000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:31096000-31107000	Weak transcription	Right Atrium	heart
3	chr6:31100600-31107000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:31105400-31107200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr6:31105400-31108000	Enhancers	Esophagus	oesophagus
6	chr6:31105400-31108200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:31105600-31107000	Weak transcription	HUVEC	blood vessel
8	chr6:31105600-31107200	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr6:31105600-31107200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr6:31105600-31108000	Enhancers	H9 Cell Line	embryonic stem cell
11	chr6:31105600-31109800	Weak transcription	Brain Germinal Matrix	brain
12	chr6:31105600-31110000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:31105600-31110200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:31105600-31110400	Weak transcription	Fetal Lung	lung
15	chr6:31105600-31124400	Weak transcription	Fetal Kidney	kidney
16	chr6:31105600-31124800	Weak transcription	Small Intestine	intestine
17	chr6:31105800-31106800	Weak transcription	Left Ventricle	heart
18	chr6:31105800-31106800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr6:31105800-31107000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:31105800-31107000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:31105800-31107000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:31105800-31107000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:31105800-31107000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr6:31105800-31107000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:31105800-31107000	Weak transcription	Fetal Heart	heart
26	chr6:31105800-31107000	Weak transcription	Spleen	Spleen
27	chr6:31105800-31107000	Weak transcription	NHEK	skin
28	chr6:31105800-31107200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:31105800-31107200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:31105800-31107200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr6:31105800-31107200	Weak transcription	HSMM	muscle
32	chr6:31105800-31107200	Weak transcription	NH-A	brain
33	chr6:31105800-31107600	Enhancers	Fetal Muscle Trunk	muscle
34	chr6:31105800-31107600	Enhancers	Stomach Mucosa	stomach
35	chr6:31105800-31108000	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr6:31105800-31108800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr6:31105800-31109000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:31105800-31109600	Weak transcription	Thymus	Thymus
39	chr6:31105800-31109800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr6:31105800-31109800	Weak transcription	Liver	Liver
41	chr6:31105800-31110200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:31105800-31110200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr6:31105800-31110200	Weak transcription	Adipose Nuclei	Adipose
44	chr6:31105800-31110200	Weak transcription	Brain Anterior Caudate	brain
45	chr6:31105800-31110200	Weak transcription	Brain Hippocampus Middle	brain
46	chr6:31105800-31110200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr6:31105800-31110400	Weak transcription	Primary T cells from cord blood	blood
48	chr6:31105800-31110400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr6:31105800-31110400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:31105800-31110400	Weak transcription	Brain Angular Gyrus	brain

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