Variant report

Variant	rs584828
Chromosome Location	chr17:38599230-38599231
allele	A/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	MAX	chr17:38598612-38602497	A549	lung:	n/a	chr17:38599856-38599866
2	CTCF	chr17:38599080-38599230	GM12873	blood:	n/a	n/a
3	YY1	chr17:38599105-38599305	K562	blood:	n/a	n/a
4	BCL3	chr17:38598687-38599634	A549	lung:	n/a	chr17:38599413-38599426
5	SIX5	chr17:38598624-38599522	A549	lung:	n/a	n/a
6	CTCF	chr17:38599220-38599370	HCPEpiC	choroid plexus:	n/a	n/a
7	CBX3	chr17:38598667-38599361	K562	blood:	n/a	n/a
8	CTCF	chr17:38599180-38599330	HCM	heart:	n/a	n/a
9	TEAD4	chr17:38598792-38599304	K562	blood:	n/a	n/a
10	E2F6	chr17:38598792-38600332	A549	lung:	n/a	chr17:38599127-38599139 chr17:38599728-38599737
11	POLR2A	chr17:38599127-38601091	A549	lung:	n/a	n/a
12	NR2F2	chr17:38598816-38599547	MCF-7	breast:	n/a	n/a
13	CTCF	chr17:38599200-38599350	HMF	breast:	n/a	n/a
14	POLR2A	chr17:38599081-38600304	NB4	blood:	n/a	n/a
15	CTCF	chr17:38599100-38599250	HepG2	liver:	n/a	n/a
16	POLR2A	chr17:38599172-38599559	K562	blood:	n/a	n/a
17	CTCF	chr17:38599180-38599330	HEEpiC	esophagus:	n/a	n/a
18	CTCF	chr17:38599200-38599350	K562	blood:	n/a	n/a
19	CTCF	chr17:38599100-38599250	AoAF	blood vessel:	n/a	n/a
20	TAF1	chr17:38599220-38599927	A549	lung:	n/a	n/a
21	MAZ	chr17:38598638-38602479	IMR90	lung:	n/a	chr17:38599856-38599866
22	EGR1	chr17:38598880-38599418	MCF-7	breast:	n/a	chr17:38599124-38599134 chr17:38599124-38599134 chr17:38599121-38599136 chr17:38599122-38599135 chr17:38599125-38599135 chr17:38599122-38599135 chr17:38599123-38599134 chr17:38599118-38599140 chr17:38599122-38599135 chr17:38599125-38599134 chr17:38599122-38599136 chr17:38599122-38599135
23	REST	chr17:38598745-38599611	A549	lung:	n/a	chr17:38599288-38599297 chr17:38599043-38599056 chr17:38599270-38599280
24	POLR2A	chr17:38598990-38600252	K562	blood:	n/a	n/a
25	CTCF	chr17:38599200-38599350	AG10803	skin:	n/a	n/a
26	JUND	chr17:38598790-38599516	K562	blood:	n/a	chr17:38598817-38598828 chr17:38599373-38599382
27	SMC3	chr17:38599162-38601066	SK-N-SH	brain:	n/a	chr17:38599730-38599740
28	EGR1	chr17:38598885-38599332	K562	blood:	n/a	chr17:38599124-38599134 chr17:38599124-38599134 chr17:38599121-38599136 chr17:38599122-38599135 chr17:38599125-38599135 chr17:38599122-38599135 chr17:38599123-38599134 chr17:38599118-38599140 chr17:38599122-38599135 chr17:38599125-38599134 chr17:38599122-38599136 chr17:38599122-38599135
29	CTCF	chr17:38599160-38599310	AG04449	skin:	n/a	n/a
30	CTCF	chr17:38598478-38602583	A549	lung:	n/a	n/a
31	POLR2A	chr17:38598937-38600627	MCF-7	breast:	n/a	n/a
32	SP1	chr17:38598759-38599889	A549	lung:	n/a	chr17:38599373-38599385 chr17:38599375-38599384 chr17:38599373-38599385 chr17:38599713-38599727 chr17:38599706-38599720 chr17:38599652-38599662 chr17:38599127-38599136 chr17:38599652-38599662
33	EP300	chr17:38599189-38599247	K562	blood:	n/a	n/a
34	CTCF	chr17:38599140-38599290	AG09319	gingival:	n/a	n/a
35	POLR2A	chr17:38598935-38600621	PFSK-1	brain:	n/a	n/a
36	MAX	chr17:38598727-38600587	A549	lung:	n/a	chr17:38599856-38599866
37	POLR2A	chr17:38598691-38600986	MCF-7	breast:	n/a	n/a
38	CTCF	chr17:38599140-38599290	HPAF	blood vessel:	n/a	n/a
39	TBP	chr17:38599214-38600140	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr17:38599025-38599388	MCF-7	breast:	n/a	n/a
41	HMGN3	chr17:38598981-38600351	K562	blood:	n/a	n/a
42	CTCF	chr17:38599080-38599230	NHEK	skin:	n/a	n/a
43	NR2F2	chr17:38598959-38599484	MCF-7	breast:	n/a	n/a
44	CTCF	chr17:38599160-38599310	HVMF	connective:	n/a	n/a
45	MXI1	chr17:38599133-38601270	SK-N-SH	brain:	n/a	n/a
46	CTCF	chr17:38599200-38599350	BJ	skin:	n/a	n/a
47	ELF1	chr17:38598937-38599457	A549	lung:	n/a	chr17:38599313-38599325 chr17:38599125-38599137
48	RAD21	chr17:38598903-38600699	SK-N-SH	brain:	n/a	chr17:38599707-38599719 chr17:38599886-38599900 chr17:38599709-38599719 chr17:38599888-38599902
49	MAZ	chr17:38598930-38600285	K562	blood:	n/a	chr17:38599856-38599866
50	FOSL2	chr17:38598553-38599469	A549	lung:	n/a	chr17:38599373-38599382

No.	Distal block	Cell Line	Cell type
1	chr17:38461615..38484404-chr17:38597525..38608992,85	MCF-7	breast:
2	chr17:38597471..38599668-chr17:38689776..38691457,2	K562	blood:
3	chr17:38571221..38576195-chr17:38597437..38603899,8	K562	blood:
4	chr17:38507026..38508719-chr17:38598987..38601879,2	K562	blood:
5	chr17:38555377..38556004-chr17:38599008..38599961,2	K562	blood:
6	chr17:38598881..38602329-chr17:38713858..38720847,8	MCF-7	breast:
7	chr17:38518063..38521220-chr17:38597683..38601473,5	MCF-7	breast:
8	chr17:38597908..38601053-chr17:38654458..38659532,5	MCF-7	breast:
9	chr17:38336165..38338939-chr17:38598006..38600043,2	MCF-7	breast:
10	chr17:38598261..38600683-chr9:136220142..136221734,2	MCF-7	breast:
11	chr17:38572047..38583621-chr17:38597341..38605150,24	MCF-7	breast:

Variant related genes	Relation type
IGFBP4	TF binding region
ENSG00000240125	TF binding region
ENSG00000131746	Chromatin interaction
ENSG00000148290	Chromatin interaction
ENSG00000183153	Chromatin interaction
ENSG00000131747	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000126353	Chromatin interaction
ENSG00000108352	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1009570	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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10852940	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11078945	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11657212	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1868758	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2015561	0.90[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35103116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4890114	0.81[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs56394376	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs584438	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598892	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632224	0.93[EUR][1000 genomes];0.97[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	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv908223	chr17:38530799-38609187	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3442525	chr17:38598451-38601299	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	esv3384974	chr17:38598726-38601149	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs584828	MMP28	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38584600-38600200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr17:38598600-38599400	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr17:38598600-38599400	Flanking Active TSS	A549	lung
4	chr17:38598800-38599400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
5	chr17:38598800-38599400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr17:38598800-38599400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr17:38598800-38599400	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr17:38598800-38599400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr17:38598800-38599400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr17:38598800-38599400	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr17:38598800-38599400	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr17:38598800-38599400	Flanking Active TSS	Colon Smooth Muscle	Colon
13	chr17:38598800-38599400	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr17:38598800-38599400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr17:38598800-38599400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr17:38598800-38599400	Flanking Active TSS	K562	blood
17	chr17:38598800-38599400	Flanking Active TSS	NHLF	lung
18	chr17:38598800-38599400	Flanking Active TSS	Osteobl	bone
19	chr17:38598800-38599600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr17:38598800-38599600	Flanking Active TSS	Colonic Mucosa	Colon
21	chr17:38598800-38599600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr17:38598800-38599600	Flanking Active TSS	Dnd41	blood
23	chr17:38598800-38599800	Active TSS	Primary hematopoietic stem cells	blood
24	chr17:38598800-38600800	Active TSS	Brain Angular Gyrus	brain
25	chr17:38598800-38601400	Weak transcription	Hela-S3	cervix
26	chr17:38598800-38601800	Active TSS	H9 Cell Line	embryonic stem cell
27	chr17:38599000-38599400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr17:38599000-38599400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr17:38599000-38599400	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr17:38599000-38599400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr17:38599000-38599400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr17:38599000-38599400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr17:38599000-38599400	Flanking Active TSS	Liver	Liver
34	chr17:38599000-38599400	Flanking Active TSS	Brain Germinal Matrix	brain
35	chr17:38599000-38599400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr17:38599000-38599400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr17:38599000-38599400	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr17:38599000-38599400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
39	chr17:38599000-38599400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
40	chr17:38599000-38599400	Flanking Active TSS	Fetal Lung	lung
41	chr17:38599000-38599400	Flanking Active TSS	Fetal Stomach	stomach
42	chr17:38599000-38599400	Flanking Active TSS	Left Ventricle	heart
43	chr17:38599000-38599400	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr17:38599000-38599400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr17:38599000-38599400	Flanking Active TSS	Spleen	Spleen
46	chr17:38599000-38599400	Flanking Active TSS	HSMMtube	muscle
47	chr17:38599000-38599400	Flanking Active TSS	HUVEC	blood vessel
48	chr17:38599000-38599400	Flanking Active TSS	NH-A	brain
49	chr17:38599000-38599400	Flanking Active TSS	NHDF-Ad	bronchial
50	chr17:38599000-38599400	Flanking Bivalent TSS/Enh	NHEK	skin

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