Variant report

Variant	rs4727459
Chromosome Location	chr7:100276821-100276822
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:100031079..100034437-chr7:100276731..100280663,4	MCF-7	breast:
2	chr7:100276399..100279739-chr7:100472420..100474901,3	MCF-7	breast:
3	chr7:100264149..100265657-chr7:100276050..100278682,2	MCF-7	breast:
4	chr7:100208313..100211642-chr7:100274412..100277175,3	MCF-7	breast:
5	chr7:100275467..100278687-chr7:100485492..100488465,4	MCF-7	breast:
6	chr7:100178369..100186125-chr7:100269651..100278553,26	MCF-7	breast:
7	chr7:100200926..100203501-chr7:100276170..100279769,4	MCF-7	breast:
8	chr7:100235578..100238290-chr7:100275939..100277984,2	K562	blood:
9	chr7:100080151..100081668-chr7:100276623..100279323,2	MCF-7	breast:
10	chr7:100182665..100186013-chr7:100275619..100278332,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000266372	Chromatin interaction
ENSG00000106333	Chromatin interaction
ENSG00000160813	Chromatin interaction
ENSG00000241357	Chromatin interaction
ENSG00000176125	Chromatin interaction
ENSG00000087087	Chromatin interaction
ENSG00000166924	Chromatin interaction
ENSG00000224729	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000106330	Chromatin interaction
ENSG00000077454	Chromatin interaction
ENSG00000240211	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10277087	0.89[JPT][hapmap]
rs10487157	0.81[CHB][hapmap];0.85[MEX][hapmap]
rs10953300	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953301	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11520986	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11760602	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11764045	0.81[CHB][hapmap];0.85[MEX][hapmap]
rs11765509	0.91[EUR][1000 genomes]
rs11769012	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11772052	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11772705	0.84[ASN][1000 genomes]
rs11772849	0.92[EUR][1000 genomes]
rs11973874	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11974395	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979818	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11980509	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11983334	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11984421	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12531792	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532878	0.81[CHB][hapmap];0.85[MEX][hapmap]
rs1734908	0.89[JPT][hapmap]
rs2075671	0.83[CHB][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs2075674	0.81[CHB][hapmap];0.90[MEX][hapmap]
rs221790	0.89[JPT][hapmap]
rs221795	0.89[JPT][hapmap]
rs221801	0.89[JPT][hapmap]
rs2231170	0.81[CHB][hapmap]
rs2231172	0.81[CHB][hapmap];0.90[MEX][hapmap]
rs2272572	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2293769	0.83[CHB][hapmap]
rs4729601	0.81[CHB][hapmap]
rs4729602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4729605	0.91[EUR][1000 genomes]
rs4729606	0.95[CEU][hapmap];0.83[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs4729607	0.95[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs504141	0.89[JPT][hapmap]
rs507392	0.89[JPT][hapmap]
rs551238	0.89[JPT][hapmap]
rs62482249	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482250	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482251	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62482252	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62483567	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62483569	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62483570	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6942733	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs6969584	0.85[MEX][hapmap]
rs6969697	0.85[MEX][hapmap]
rs7812123	0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
3	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv888791	chr7:100221867-100371114	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv607933	chr7:100240191-100365613	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
9	nsv8184	chr7:100240737-100345945	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	nsv888792	chr7:100252918-100329189	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv888793	chr7:100266081-100279163	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv888794	chr7:100266081-100283261	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv888795	chr7:100266081-100298626	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	31 gene(s)	inside rSNPs	diseases
14	esv1804951	chr7:100275135-100374093	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4727459	TSC22D4	cis	parietal	SCAN
rs4727459	DLX5	cis	cerebellum	SCAN
rs4727459	GIGYF1	cis	lymphoblastoid	seeQTL
rs4727459	PERQ1	cis	multi-tissue	Pritchard
rs4727459	MOSPD3	cis	Whole Blood	GTEx
rs4727459	PERQ1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100272800-100277400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:100273200-100277400	Enhancers	Fetal Heart	heart
3	chr7:100273600-100277800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:100274000-100283600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:100274000-100287000	Strong transcription	Lung	lung
6	chr7:100274200-100277000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:100274200-100277000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr7:100274200-100278400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr7:100274200-100278800	Genic enhancers	Primary monocytes fromperipheralblood	blood
10	chr7:100274200-100280000	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr7:100274200-100287600	Strong transcription	Placenta Amnion	Placenta Amnion
12	chr7:100274200-100288800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:100274200-100289200	Weak transcription	Fetal Kidney	kidney
14	chr7:100274200-100290400	Weak transcription	HSMMtube	muscle
15	chr7:100274400-100277000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:100274400-100277000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr7:100274400-100277000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr7:100274400-100277000	Strong transcription	Esophagus	oesophagus
19	chr7:100274400-100277000	Weak transcription	NH-A	brain
20	chr7:100274400-100277200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:100274400-100277200	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr7:100274400-100277200	Weak transcription	Right Atrium	heart
23	chr7:100274400-100277200	Strong transcription	NHDF-Ad	bronchial
24	chr7:100274400-100277200	Strong transcription	NHLF	lung
25	chr7:100274400-100277400	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr7:100274400-100277600	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr7:100274400-100278400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
28	chr7:100274400-100278400	Strong transcription	Aorta	Aorta
29	chr7:100274400-100278400	Genic enhancers	Fetal Intestine Large	intestine
30	chr7:100274400-100278600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr7:100274400-100278600	Strong transcription	Fetal Stomach	stomach
32	chr7:100274400-100279600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:100274400-100279600	Strong transcription	HMEC	breast
34	chr7:100274400-100280000	Weak transcription	HSMM	muscle
35	chr7:100274400-100280400	Strong transcription	HUVEC	blood vessel
36	chr7:100274400-100284000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr7:100274400-100284800	Strong transcription	Osteobl	bone
38	chr7:100274400-100285400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr7:100274400-100286000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr7:100274400-100286200	Strong transcription	Left Ventricle	heart
41	chr7:100274400-100286200	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr7:100274400-100286400	Strong transcription	Thymus	Thymus
43	chr7:100274400-100287400	Strong transcription	Brain Cingulate Gyrus	brain
44	chr7:100274400-100287400	Strong transcription	Brain Substantia Nigra	brain
45	chr7:100274400-100287600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:100274400-100287800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr7:100274400-100287800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr7:100274400-100287800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr7:100274400-100288000	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr7:100274400-100288000	Strong transcription	Rectal Mucosa Donor 29	rectum

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