Variant report

Variant	rs3130453
Chromosome Location	chr6:31124849-31124850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:31123925-31125568	SK-N-MC	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:31124835..31127745-chr6:31135310..31138711,4	MCF-7	breast:
2	chr6:30584033..30586510-chr6:31124123..31126779,2	K562	blood:
3	chr6:31119377..31122828-chr6:31124699..31127188,7	K562	blood:
4	chr6:31116689..31119145-chr6:31122656..31125188,2	K562	blood:
5	chr6:31103871..31105834-chr6:31123155..31127372,3	MCF-7	breast:
6	chr6:31112475..31116177-chr6:31122128..31126125,5	K562	blood:
7	chr6:31120552..31122855-chr6:31123459..31126942,6	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POU5F1-9	chr6:31124800-31124866	NONHSAT108730
2	lnc-POU5F1-9	chr6:31124800-31124866	NONHSAT108728

No data

Variant related genes	Relation type
TCF19	TF binding region
CCHCR1	TF binding region
ENSG00000204568	Chromatin interaction
ENSG00000204540	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204536	Chromatin interaction
ENSG00000204531	Chromatin interaction
ENSG00000204569	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs130066	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13409	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1419880	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2021375	0.82[AMR][1000 genomes]
rs2077010	0.90[ASN][1000 genomes]
rs3094187	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3094195	0.85[AMR][1000 genomes]
rs3095239	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3132526	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6905862	0.94[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs885950	0.85[ASN][1000 genomes]
rs885951	0.87[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	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	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
14	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
15	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
16	nsv524061	chr6:31107087-31133943	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
17	nsv884138	chr6:31114573-31129707	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3130453	SNRPC	cis	parietal	SCAN
rs3130453	CCHCR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31105800-31125200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:31106000-31125000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr6:31106000-31125000	Weak transcription	Fetal Brain Male	brain
4	chr6:31106000-31125200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:31107600-31125000	Weak transcription	NHDF-Ad	bronchial
6	chr6:31107800-31125000	Weak transcription	Fetal Heart	heart
7	chr6:31110200-31125000	Weak transcription	A549	lung
8	chr6:31111000-31125000	Weak transcription	NHEK	skin
9	chr6:31111000-31125200	Weak transcription	HSMMtube	muscle
10	chr6:31111200-31125000	Weak transcription	HUVEC	blood vessel
11	chr6:31111400-31125000	Weak transcription	Right Atrium	heart
12	chr6:31111400-31125000	Weak transcription	HMEC	breast
13	chr6:31111400-31125600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:31111600-31125000	Weak transcription	NH-A	brain
15	chr6:31112400-31125000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:31113800-31125200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:31116200-31125200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr6:31118000-31125000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr6:31118600-31125000	Weak transcription	Brain Substantia Nigra	brain
20	chr6:31118600-31125000	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:31118600-31125000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:31119000-31125000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr6:31119000-31125200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr6:31119400-31125200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr6:31119600-31125000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:31119600-31125000	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:31119600-31125000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:31119600-31125000	Weak transcription	Colonic Mucosa	Colon
29	chr6:31119600-31125200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr6:31121000-31125000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:31122400-31125000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr6:31122600-31125000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr6:31122600-31125000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:31122600-31125200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:31122600-31125200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:31122800-31125000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr6:31122800-31125000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:31122800-31125000	Weak transcription	Esophagus	oesophagus
39	chr6:31122800-31125000	Weak transcription	Thymus	Thymus
40	chr6:31122800-31125000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr6:31122800-31125200	Weak transcription	Gastric	stomach
42	chr6:31122800-31125200	Weak transcription	Left Ventricle	heart
43	chr6:31122800-31125200	Weak transcription	Lung	lung
44	chr6:31122800-31125200	Weak transcription	Ovary	ovary
45	chr6:31122800-31125200	Weak transcription	Spleen	Spleen
46	chr6:31123000-31125000	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr6:31123000-31125200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr6:31123000-31125200	Weak transcription	Adipose Nuclei	Adipose
49	chr6:31123200-31125200	Weak transcription	Placenta	Placenta
50	chr6:31123600-31125000	Weak transcription	Brain Anterior Caudate	brain

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