Variant report

Variant	rs998071
Chromosome Location	chr4:95591976-95591977
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr4:95590594-95592493	A549	lung:	n/a	chr4:95591368-95591378
2	GATA3	chr4:95591469-95592102	T-47D	breast:	n/a	n/a
3	EP300	chr4:95591072-95592177	A549	lung:	n/a	chr4:95591368-95591378
4	RAD21	chr4:95591375-95591991	A549	lung:	n/a	n/a
5	GATA3	chr4:95591839-95592261	MCF-7	breast:	n/a	n/a
6	SIX5	chr4:95591289-95592012	A549	lung:	n/a	n/a
7	SP1	chr4:95591053-95592005	A549	lung:	n/a	n/a
8	GATA3	chr4:95590773-95592640	A549	lung:	n/a	n/a
9	GATA3	chr4:95591759-95592135	MCF-7	breast:	n/a	n/a
10	TCF12	chr4:95589639-95592640	A549	lung:	n/a	n/a
11	SP1	chr4:95590820-95592118	A549	lung:	n/a	n/a
12	POLR2A	chr4:95591974-95592621	A549	lung:	n/a	n/a
13	GATA3	chr4:95591499-95592166	T-47D	breast:	n/a	n/a
14	FOXA2	chr4:95591051-95592028	A549	lung:	n/a	n/a
15	GATA3	chr4:95591795-95592024	MCF-7	breast:	n/a	n/a
16	NR2F2	chr4:95591453-95592222	MCF-7	breast:	n/a	chr4:95591987-95592002
17	FOSL2	chr4:95590473-95592317	A549	lung:	n/a	n/a
18	POLR2A	chr4:95591726-95592929	K562	blood:	n/a	n/a
19	REST	chr4:95590432-95592093	A549	lung:	n/a	n/a
20	BCL3	chr4:95589771-95592149	A549	lung:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:95585740..95587732-chr4:95591128..95592898,2	MCF-7	breast:
2	chr4:95590309..95593538-chr4:95611689..95613963,4	MCF-7	breast:
3	chr4:95591301..95592059-chr4:95611866..95612408,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000249951	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10015716	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1043848	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10590	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12500116	0.92[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12505788	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12510147	0.80[CEU][hapmap]
rs12511169	0.83[ASW][hapmap];0.82[CEU][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13121500	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1509620	0.91[LWK][hapmap]
rs17021918	0.92[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17021972	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2136486	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs2280003	0.83[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35964087	0.91[EUR][1000 genomes]
rs3762876	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699316	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61597100	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6817664	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6822544	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6837308	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7659399	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7674144	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7681843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7694162	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1005816	chr4:95573444-95902704	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95527800-95592200	Weak transcription	Pancreas	Pancrea
2	chr4:95533800-95594200	Weak transcription	Gastric	stomach
3	chr4:95537600-95592800	Weak transcription	Fetal Stomach	stomach
4	chr4:95540200-95597800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:95541200-95595600	Weak transcription	Primary T cells from cord blood	blood
6	chr4:95564000-95595000	Weak transcription	NHDF-Ad	bronchial
7	chr4:95570800-95599800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:95573600-95595000	Weak transcription	Small Intestine	intestine
9	chr4:95576200-95598000	Weak transcription	Aorta	Aorta
10	chr4:95576200-95598200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:95578600-95593800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:95579000-95592400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:95580000-95597800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:95582000-95595400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr4:95582000-95599800	Weak transcription	NHEK	skin
16	chr4:95582400-95592200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:95582400-95594200	Weak transcription	Esophagus	oesophagus
18	chr4:95582400-95596200	Weak transcription	Fetal Muscle Leg	muscle
19	chr4:95582400-95598200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:95582600-95593800	Weak transcription	Ovary	ovary
21	chr4:95582600-95600000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:95582800-95598000	Weak transcription	Fetal Heart	heart
23	chr4:95585000-95592200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:95585200-95592200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:95585200-95592200	Weak transcription	Adipose Nuclei	Adipose
26	chr4:95585200-95593600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr4:95585200-95598200	Weak transcription	Colon Smooth Muscle	Colon
28	chr4:95586000-95594000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr4:95586000-95598000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:95586600-95594000	Weak transcription	Fetal Intestine Small	intestine
31	chr4:95586600-95594200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:95587400-95598000	Weak transcription	HSMMtube	muscle
33	chr4:95587600-95592200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:95587600-95592200	Weak transcription	Left Ventricle	heart
35	chr4:95587800-95598400	Weak transcription	HSMM	muscle
36	chr4:95588000-95598400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr4:95588000-95599800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:95588200-95595200	Weak transcription	Placenta	Placenta
39	chr4:95588600-95594200	Weak transcription	Psoas Muscle	Psoas
40	chr4:95589800-95597600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:95589800-95598000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr4:95590000-95599800	Weak transcription	NH-A	brain
43	chr4:95590200-95592200	Enhancers	HUVEC	blood vessel
44	chr4:95590200-95599800	Weak transcription	HMEC	breast
45	chr4:95590400-95592400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:95590800-95592600	Flanking Active TSS	A549	lung
47	chr4:95590800-95601200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:95591200-95592000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:95591200-95594200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:95591400-95593800	Weak transcription	Fetal Kidney	kidney

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