Variant report

Variant	rs30611
Chromosome Location	chr5:14415053-14415054
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXM1	chr5:14414723-14416536	GM12878	blood:	n/a	n/a
2	MTA3	chr5:14414804-14416482	GM12878	blood:	n/a	n/a
3	YY1	chr5:14415026-14415854	GM12878	blood:	n/a	n/a
4	STAT5A	chr5:14414908-14415823	GM12878	blood:	n/a	n/a
5	STAT3	chr5:14414956-14416111	GM12878	blood:	n/a	n/a
6	BCLAF1	chr5:14414714-14416076	GM12878	blood:	n/a	chr5:14416067-14416076
7	TBP	chr5:14414792-14415773	GM12878	blood:	n/a	n/a
8	NFATC1	chr5:14414874-14416307	GM12878	blood:	n/a	n/a
9	CREB1	chr5:14414709-14416668	GM12878	blood:	n/a	n/a
10	EP300	chr5:14414997-14416232	GM12878	blood:	n/a	chr5:14416056-14416065
11	PML	chr5:14414497-14416304	GM12878	blood:	n/a	n/a
12	EP300	chr5:14414959-14416269	GM12878	blood:	n/a	chr5:14416056-14416065
13	EP300	chr5:14414711-14415726	GM12878	blood:	n/a	n/a
14	RUNX3	chr5:14414303-14416683	GM12878	blood:	n/a	n/a
15	NFIC	chr5:14414555-14416672	GM12878	blood:	n/a	n/a
16	BATF	chr5:14414968-14415407	GM12878	blood:	n/a	n/a
17	EBF1	chr5:14414842-14415706	GM12878	blood:	n/a	n/a
18	CUX1	chr5:14414800-14416287	GM12878	blood:	n/a	n/a
19	BCLAF1	chr5:14414847-14416018	GM12878	blood:	n/a	n/a
20	MAZ	chr5:14414920-14415416	GM12878	blood:	n/a	n/a
21	EBF1	chr5:14414973-14416639	GM12878	blood:	n/a	n/a
22	MEF2A	chr5:14414948-14415510	GM12878	blood:	n/a	n/a
23	ATF2	chr5:14414726-14416727	GM12878	blood:	n/a	n/a
24	RUNX3	chr5:14414469-14416316	GM12878	blood:	n/a	n/a
25	PAX5	chr5:14414927-14415855	GM12878	blood:	n/a	chr5:14415635-14415645
26	NFATC1	chr5:14414788-14416606	GM12878	blood:	n/a	n/a
27	POLR2A	chr5:14414714-14416010	GM12878	blood:	n/a	n/a
28	POU2F2	chr5:14414913-14415795	GM12878	blood:	n/a	chr5:14415696-14415709
29	POLR2A	chr5:14414841-14415808	GM12878	blood:	n/a	n/a
30	CEBPB	chr5:14414883-14416325	GM12878	blood:	n/a	n/a
31	WRNIP1	chr5:14414908-14415732	GM12878	blood:	n/a	n/a
32	IRF4	chr5:14415015-14415458	GM12878	blood:	n/a	n/a
33	MTA3	chr5:14414368-14416321	GM12878	blood:	n/a	n/a
34	POLR2A	chr5:14412830-14415455	U87	brain:	n/a	n/a
35	POLR2A	chr5:14414738-14415424	U87	brain:	n/a	n/a
36	BCL11A	chr5:14414946-14416213	GM12878	blood:	n/a	chr5:14416067-14416076
37	CHD2	chr5:14414965-14416316	GM12878	blood:	n/a	n/a
38	JUND	chr5:14414700-14416473	GM12878	blood:	n/a	chr5:14416056-14416065 chr5:14415968-14415978 chr5:14416058-14416065 chr5:14415191-14415203
39	NFIC	chr5:14414769-14416566	GM12878	blood:	n/a	n/a
40	STAT5A	chr5:14414783-14416320	GM12878	blood:	n/a	chr5:14414865-14414888
41	RCOR1	chr5:14414929-14416260	GM12878	blood:	n/a	n/a
42	FOXM1	chr5:14414709-14416451	GM12878	blood:	n/a	n/a
43	BCL11A	chr5:14415050-14415363	GM12878	blood:	n/a	n/a
44	IRF4	chr5:14414909-14415755	GM12878	blood:	n/a	n/a
45	BATF	chr5:14414922-14416242	GM12878	blood:	n/a	n/a
46	BHLHE40	chr5:14414797-14416242	GM12878	blood:	n/a	n/a
47	POLR2A	chr5:14414894-14416031	GM12878	blood:	n/a	n/a
48	TBL1XR1	chr5:14414854-14415714	GM12878	blood:	n/a	n/a
49	BCL3	chr5:14414928-14416500	GM12878	blood:	n/a	chr5:14416067-14416076
50	ATF2	chr5:14414877-14416577	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:14407920..14412107-chr5:14413885..14416299,3	MCF-7	breast:
2	chr5:14414154..14415696-chr5:14664055..14665820,2	MCF-7	breast:
3	chr5:14413016..14415432-chr5:14426499..14428119,2	MCF-7	breast:

Variant related genes	Relation type
TRIO	TF binding region
ENSG00000154124	Chromatin interaction
ENSG00000261360	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11955578	1.00[JPT][hapmap]
rs11957060	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11957857	0.88[ASN][1000 genomes]
rs13356126	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs173947	0.89[ASN][1000 genomes]
rs187190	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs187667	0.89[ASN][1000 genomes]
rs247136	0.91[ASN][1000 genomes]
rs256412	0.85[ASN][1000 genomes]
rs26187	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28018	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28343	0.89[ASN][1000 genomes]
rs30606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs30607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs30608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs30609	0.98[ASN][1000 genomes]
rs30610	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30773	0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs30774	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs30786	1.00[JPT][hapmap]
rs30787	1.00[JPT][hapmap]
rs30788	1.00[JPT][hapmap]
rs30789	1.00[JPT][hapmap]
rs30790	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs30791	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs30794	1.00[JPT][hapmap]
rs30795	1.00[JPT][hapmap]
rs30800	0.89[ASN][1000 genomes]
rs30801	0.89[ASN][1000 genomes]
rs358752	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs378369	0.89[ASN][1000 genomes]
rs382403	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs389729	1.00[ASW][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs397319	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs40278	0.89[ASN][1000 genomes]
rs40572	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[ASN][1000 genomes]
rs42206	0.89[ASN][1000 genomes]
rs42404	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs42555	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[ASN][1000 genomes]
rs42556	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs890937	0.94[AMR][1000 genomes];0.92[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	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14357600-14422000	Weak transcription	Stomach Mucosa	stomach
2	chr5:14363800-14430600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr5:14363800-14430600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr5:14392400-14426800	Weak transcription	Psoas Muscle	Psoas
5	chr5:14399000-14419800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:14399600-14416400	Strong transcription	Duodenum Mucosa	Duodenum
7	chr5:14400800-14416000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:14404000-14420600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr5:14404400-14428600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:14404600-14427600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:14404800-14416200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:14404800-14417200	Strong transcription	HSMMtube	muscle
13	chr5:14404800-14424000	Strong transcription	Liver	Liver
14	chr5:14405200-14415600	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:14405200-14423600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:14405400-14416000	Strong transcription	Lung	lung
17	chr5:14405400-14423400	Strong transcription	Placenta	Placenta
18	chr5:14406200-14416200	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr5:14406400-14416200	Strong transcription	Hela-S3	cervix
20	chr5:14406800-14420000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:14406800-14421600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:14407000-14416800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr5:14407000-14417000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr5:14407200-14416400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:14407200-14418800	Strong transcription	NHEK	skin
26	chr5:14407600-14417000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr5:14407800-14415800	Strong transcription	Adipose Nuclei	Adipose
28	chr5:14407800-14418000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:14407800-14419800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr5:14409000-14415600	Genic enhancers	Fetal Muscle Trunk	muscle
31	chr5:14409000-14416200	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr5:14409200-14416800	Strong transcription	A549	lung
33	chr5:14409400-14415800	Strong transcription	HepG2	liver
34	chr5:14409800-14415800	Strong transcription	Stomach Smooth Muscle	stomach
35	chr5:14410000-14416000	Strong transcription	Left Ventricle	heart
36	chr5:14410200-14416400	Strong transcription	HMEC	breast
37	chr5:14410400-14415400	Weak transcription	Esophagus	oesophagus
38	chr5:14410600-14415200	Weak transcription	Brain Angular Gyrus	brain
39	chr5:14410600-14415800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr5:14410600-14428000	Weak transcription	Fetal Heart	heart
41	chr5:14410800-14415600	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr5:14411000-14428200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr5:14411200-14423600	Strong transcription	Fetal Intestine Large	intestine
44	chr5:14411800-14415800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr5:14412000-14415400	Weak transcription	Ovary	ovary
46	chr5:14412000-14416200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr5:14412000-14429600	Strong transcription	Fetal Intestine Small	intestine
48	chr5:14412200-14415800	Strong transcription	Spleen	Spleen
49	chr5:14412400-14415600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr5:14412400-14416400	Genic enhancers	NH-A	brain

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