Variant report

Variant	rs10456351
Chromosome Location	chr6:26986792-26986793
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:10)
LncRNA
region (count:1)
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	chr6:26986701-26988296	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26986672..26989789-chr6:27000178..27003902,5	K562	blood:
2	chr6:26985450..26988105-chr6:27045850..27047500,2	MCF-7	breast:
3	chr6:26986141..26989315-chr6:27099693..27102722,3	K562	blood:
4	chr6:26984517..26987558-chr6:27114844..27118059,3	K562	blood:
5	chr6:26596362..26598030-chr6:26986586..26989465,2	MCF-7	breast:
6	chr6:26986048..26988342-chr8:145752952..145755516,2	MCF-7	breast:
7	chr6:26969414..26971961-chr6:26985558..26987515,2	K562	blood:
8	chr6:26923074..26925467-chr6:26986570..26988926,2	K562	blood:
9	chr6:26595477..26598975-chr6:26986599..26989051,3	K562	blood:
10	chr6:26985479..26987950-chr6:27115470..27119189,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HIST1H2BJ-8	chr6:26985858-26989416	NONHSAT108322

No data

Variant related genes	Relation type
TRNAI2	TF binding region
LINC00240	TF binding region
ENSG00000213563	Chromatin interaction
ENSG00000272312	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000220581	Chromatin interaction
ENSG00000224843	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000241549	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10456352	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946891	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10946892	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10946893	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10946897	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946898	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11754305	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11756275	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12193875	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12201034	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12201393	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12209886	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12211984	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213438	0.83[AMR][1000 genomes]
rs12523820	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12527111	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12527231	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13212021	0.91[ASN][1000 genomes]
rs13217675	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2057348	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2142685	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2393915	0.86[ASN][1000 genomes]
rs35691005	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3999229	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4269366	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4403259	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4422620	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4424065	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4434464	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4476823	0.84[ASN][1000 genomes]
rs4509113	0.91[ASN][1000 genomes]
rs4583981	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713066	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62401067	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62402054	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456767	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6456768	0.87[ASN][1000 genomes]
rs6910264	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6930508	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6937880	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7451149	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7739845	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7747454	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7768407	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379955	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9379956	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379958	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393789	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9461330	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9467936	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467978	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs994691	0.90[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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	esv2758038	chr6:26695219-27095714	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
3	esv2759410	chr6:26695219-27095714	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
4	nsv1029124	chr6:26825468-27109774	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	244 gene(s)	inside rSNPs	diseases
5	nsv469610	chr6:26841083-26999230	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv482509	chr6:26841083-26999230	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv471636	chr6:26841084-27038175	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv469675	chr6:26848950-27015598	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv482429	chr6:26848950-27015598	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv830616	chr6:26859097-27030476	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	esv1793267	chr6:26864376-26987405	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	esv1811325	chr6:26869783-26987405	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	esv1795223	chr6:26877074-26987205	Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	esv1809024	chr6:26877074-26987205	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	esv1810582	chr6:26889428-26990246	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
16	nsv469625	chr6:26893739-27038175	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
17	nsv482537	chr6:26893739-27038175	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
18	esv15177	chr6:26916403-26987915	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10456351	RP11-457M11.5	cis	Esophagus Muscularis	GTEx
rs10456351	RP11-457M11.5	cis	Heart Left Ventricle	GTEx
rs10456351	RP11-457M11.5	cis	Skin Sun Exposed Lower leg	GTEx
rs10456351	RP11-457M11.5	cis	Thyroid	GTEx
rs10456351	RP11-457M11.5	cis	Nerve Tibial	GTEx
rs10456351	RP11-457M11.5	cis	Esophagus Mucosa	GTEx
rs10456351	RP11-457M11.5	cis	Whole Blood	GTEx
rs10456351	RP11-457M11.5	cis	Stomach	GTEx
rs10456351	RP11-457M11.5	cis	lung	GTEx
rs10456351	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs10456351	RP11-457M11.5	cis	Artery Tibial	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26976800-26987400	Weak transcription	Pancreas	Pancrea
2	chr6:26977000-26987000	Weak transcription	Ovary	ovary
3	chr6:26979200-26986800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:26985600-26987200	Weak transcription	Aorta	Aorta
5	chr6:26986000-26987000	Flanking Active TSS	K562	blood
6	chr6:26986200-26987000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:26986200-26988600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr6:26986200-26988600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:26986200-26988800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr6:26986400-26986800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:26986400-26986800	ZNF genes & repeats	Brain Substantia Nigra	brain
12	chr6:26986400-26987000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:26986400-26987000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:26986400-26988400	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr6:26986400-26988600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:26986400-26988800	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr6:26986400-26988800	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr6:26986600-26986800	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr6:26986600-26986800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:26986600-26986800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:26986600-26986800	Active TSS	Colon Smooth Muscle	Colon
22	chr6:26986600-26986800	Active TSS	Fetal Brain Male	brain
23	chr6:26986600-26986800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr6:26986600-26986800	Enhancers	NHEK	skin
25	chr6:26986600-26987000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr6:26986600-26987000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr6:26986600-26987000	Enhancers	Stomach Mucosa	stomach
28	chr6:26986600-26987000	Flanking Active TSS	A549	lung
29	chr6:26986600-26987200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr6:26986600-26987400	Flanking Active TSS	HMEC	breast
31	chr6:26986600-26988200	Active TSS	Hela-S3	cervix
32	chr6:26986600-26988400	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr6:26986600-26988600	Active TSS	H1 Cell Line	embryonic stem cell
34	chr6:26986600-26988600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:26986600-26988600	Active TSS	Brain Cingulate Gyrus	brain
36	chr6:26986600-26988600	Active TSS	Brain Hippocampus Middle	brain
37	chr6:26986600-26988600	Active TSS	Fetal Brain Female	brain
38	chr6:26986600-26988600	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr6:26986600-26988600	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr6:26986600-26988600	Active TSS	Stomach Smooth Muscle	stomach

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