Variant report

Variant	rs1718886
Chromosome Location	chr4:57849251-57849252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr4:57849012-57849332	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:57848957-57849388	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:57849127..57850775-chr4:57862388..57864850,2	K562	blood:
2	chr4:57771524..57779492-chr4:57841270..57849741,26	K562	blood:
3	chr4:57848130..57850979-chr4:57885683..57887962,2	K562	blood:
4	chr4:57849127..57851147-chr4:57863350..57865487,2	K562	blood:
5	chr4:57847527..57849310-chr4:57850020..57851620,2	MCF-7	breast:
6	chr4:57849114..57851470-chr4:57866273..57869117,2	K562	blood:
7	chr4:57842821..57845222-chr4:57848302..57852353,5	MCF-7	breast:

No data

Variant related genes	Relation type
NOA1	TF binding region
ENSG00000047315	Chromatin interaction
ENSG00000084092	Chromatin interaction
ENSG00000084093	Chromatin interaction
ENSG00000251703	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11133470	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12621	0.92[CEU][hapmap];0.95[GIH][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap]
rs1277284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1277287	0.81[TSI][hapmap]
rs1277308	0.92[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap]
rs1277311	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[TSI][hapmap]
rs1403233	0.87[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap]
rs1625691	0.81[TSI][hapmap]
rs1713997	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1718831	0.87[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap]
rs1718837	0.81[TSI][hapmap]
rs1718839	0.88[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs1718882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2293175	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412772	1.00[JPT][hapmap]
rs2948348	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34576794	0.83[EUR][1000 genomes]
rs35982175	0.83[ASN][1000 genomes]
rs3796531	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.91[ASN][1000 genomes]
rs6841086	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs6843644	0.92[CEU][hapmap];0.95[GIH][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap]
rs7668814	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs781665	0.83[EUR][1000 genomes]
rs781666	0.88[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs781668	0.88[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1718886	POLR2B	cis	cerebellum	SCAN
rs1718886	POLR2B	cis	parietal	SCAN
rs1718886	IGFBP7	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57846000-57849400	Enhancers	Brain Angular Gyrus	brain
2	chr4:57846000-57852000	Weak transcription	Aorta	Aorta
3	chr4:57846000-57853600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:57846000-57855600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:57846000-57881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:57846200-57849400	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr4:57846200-57850800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:57846200-57851400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr4:57846200-57851800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:57846200-57851800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr4:57846200-57851800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:57846200-57853000	Weak transcription	Fetal Kidney	kidney
13	chr4:57846200-57853600	Weak transcription	Esophagus	oesophagus
14	chr4:57846200-57861600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr4:57846200-57861800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:57846400-57849400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr4:57846400-57849800	Enhancers	Primary T cells fromperipheralblood	blood
18	chr4:57846600-57849400	Enhancers	Small Intestine	intestine
19	chr4:57846600-57850000	Genic enhancers	Primary T cells from cord blood	blood
20	chr4:57846600-57851800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:57846600-57852200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:57846600-57853200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr4:57846600-57861200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr4:57846800-57849600	Enhancers	HepG2	liver
25	chr4:57846800-57851200	Weak transcription	Lung	lung
26	chr4:57846800-57852000	Weak transcription	NHDF-Ad	bronchial
27	chr4:57846800-57852200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:57846800-57852600	Weak transcription	HSMMtube	muscle
29	chr4:57846800-57900000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:57847000-57850000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:57847000-57850200	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr4:57847000-57851400	Weak transcription	Right Atrium	heart
33	chr4:57847000-57851600	Weak transcription	Placenta	Placenta
34	chr4:57847000-57851600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr4:57847000-57853000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr4:57847000-57853800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr4:57847000-57853800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:57847000-57861600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr4:57847200-57849600	Weak transcription	Fetal Stomach	stomach
40	chr4:57847200-57851200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr4:57847200-57851400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr4:57847200-57851400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr4:57847200-57851800	Weak transcription	Brain Anterior Caudate	brain
44	chr4:57847200-57851800	Weak transcription	Colon Smooth Muscle	Colon
45	chr4:57847200-57851800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr4:57847200-57853000	Weak transcription	Colonic Mucosa	Colon
47	chr4:57847200-57853400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:57847200-57853600	Weak transcription	Spleen	Spleen
49	chr4:57847400-57851200	Weak transcription	Fetal Muscle Leg	muscle
50	chr4:57847600-57849400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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