Variant report

Variant	rs584438
Chromosome Location	chr17:38599172-38599173
allele	A/C/G/T
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	CBX3	chr17:38598667-38599361	K562	blood:	n/a	n/a
7	TEAD4	chr17:38598792-38599304	K562	blood:	n/a	n/a
8	E2F6	chr17:38598792-38600332	A549	lung:	n/a	chr17:38599127-38599139 chr17:38599728-38599737
9	POLR2A	chr17:38599127-38601091	A549	lung:	n/a	n/a
10	NR2F2	chr17:38598816-38599547	MCF-7	breast:	n/a	n/a
11	POLR2A	chr17:38599081-38600304	NB4	blood:	n/a	n/a
12	CTCF	chr17:38599100-38599250	HepG2	liver:	n/a	n/a
13	POLR2A	chr17:38599172-38599559	K562	blood:	n/a	n/a
14	CTCF	chr17:38599100-38599250	AoAF	blood vessel:	n/a	n/a
15	MAZ	chr17:38598638-38602479	IMR90	lung:	n/a	chr17:38599856-38599866
16	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
17	REST	chr17:38598745-38599611	A549	lung:	n/a	chr17:38599288-38599297 chr17:38599043-38599056 chr17:38599270-38599280
18	POLR2A	chr17:38598990-38600252	K562	blood:	n/a	n/a
19	JUND	chr17:38598790-38599516	K562	blood:	n/a	chr17:38598817-38598828 chr17:38599373-38599382
20	SMC3	chr17:38599162-38601066	SK-N-SH	brain:	n/a	chr17:38599730-38599740
21	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
22	CTCF	chr17:38599160-38599310	AG04449	skin:	n/a	n/a
23	CTCF	chr17:38598478-38602583	A549	lung:	n/a	n/a
24	POLR2A	chr17:38598937-38600627	MCF-7	breast:	n/a	n/a
25	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
26	CTCF	chr17:38599140-38599290	AG09319	gingival:	n/a	n/a
27	POLR2A	chr17:38598935-38600621	PFSK-1	brain:	n/a	n/a
28	MAX	chr17:38598727-38600587	A549	lung:	n/a	chr17:38599856-38599866
29	POLR2A	chr17:38598691-38600986	MCF-7	breast:	n/a	n/a
30	CTCF	chr17:38599140-38599290	HPAF	blood vessel:	n/a	n/a
31	CTCF	chr17:38599060-38599210	MCF-7	breast:	n/a	n/a
32	POLR2A	chr17:38599025-38599388	MCF-7	breast:	n/a	n/a
33	HMGN3	chr17:38598981-38600351	K562	blood:	n/a	n/a
34	CTCF	chr17:38599080-38599230	NHEK	skin:	n/a	n/a
35	NR2F2	chr17:38598959-38599484	MCF-7	breast:	n/a	n/a
36	CTCF	chr17:38599160-38599310	HVMF	connective:	n/a	n/a
37	MXI1	chr17:38599133-38601270	SK-N-SH	brain:	n/a	n/a
38	ELF1	chr17:38598937-38599457	A549	lung:	n/a	chr17:38599313-38599325 chr17:38599125-38599137
39	RAD21	chr17:38598903-38600699	SK-N-SH	brain:	n/a	chr17:38599707-38599719 chr17:38599886-38599900 chr17:38599709-38599719 chr17:38599888-38599902
40	MAZ	chr17:38598930-38600285	K562	blood:	n/a	chr17:38599856-38599866
41	FOSL2	chr17:38598553-38599469	A549	lung:	n/a	chr17:38599373-38599382
42	CTCF	chr17:38599160-38599310	AG10803	skin:	n/a	n/a
43	ELF1	chr17:38598856-38599705	MCF-7	breast:	n/a	chr17:38599313-38599325 chr17:38599125-38599137
44	REST	chr17:38599153-38599506	PANC-1	pancreas:	n/a	chr17:38599288-38599297 chr17:38599270-38599280
45	TCF12	chr17:38598550-38605713	A549	lung:	n/a	chr17:38599080-38599090 chr17:38600404-38600414
46	ELF1	chr17:38598858-38599687	GM12878	blood:	n/a	chr17:38599313-38599325 chr17:38599125-38599137
47	ELF1	chr17:38598837-38599576	K562	blood:	n/a	chr17:38599313-38599325 chr17:38599125-38599137
48	ZBTB7A	chr17:38599002-38600244	K562	blood:	n/a	chr17:38599408-38599416
49	GATA3	chr17:38598946-38602544	A549	lung:	n/a	chr17:38602087-38602099 chr17:38601316-38601326 chr17:38599116-38599129 chr17:38602088-38602097 chr17:38600654-38600661 chr17:38602088-38602098 chr17:38602090-38602097
50	POLR2A	chr17:38598819-38600275	K562	blood:	n/a	n/a

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
ENSG00000240125	TF binding region
IGFBP4	TF binding region
ENSG00000183153	Chromatin interaction
ENSG00000131759	Chromatin interaction
ENSG00000108352	Chromatin interaction
ENSG00000148290	Chromatin interaction
ENSG00000126353	Chromatin interaction
ENSG00000131746	Chromatin interaction
ENSG00000131747	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];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];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10852940	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11078945	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11657212	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1868758	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2015561	0.90[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35103116	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4890114	0.81[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs56394376	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs584828	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	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632224	0.84[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

Variant related diseases (count:1)

Disease	PMID	Source
Height	23563607	GWAS catalog

Chromatin state (count:116 , 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	chr17:38598600-38599200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr17:38598600-38599200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr17:38598600-38599200	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr17:38598600-38599200	Flanking Active TSS	Rectal Smooth Muscle	rectum
6	chr17:38598600-38599400	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr17:38598600-38599400	Flanking Active TSS	A549	lung
8	chr17:38598800-38599200	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:38598800-38599200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr17:38598800-38599200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
11	chr17:38598800-38599200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr17:38598800-38599200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
13	chr17:38598800-38599200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr17:38598800-38599200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr17:38598800-38599200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr17:38598800-38599200	Flanking Active TSS	Right Atrium	heart
17	chr17:38598800-38599200	Bivalent Enhancer	HepG2	liver
18	chr17:38598800-38599200	Enhancers	HMEC	breast
19	chr17:38598800-38599400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
20	chr17:38598800-38599400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr17:38598800-38599400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr17:38598800-38599400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr17:38598800-38599400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr17:38598800-38599400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr17:38598800-38599400	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr17:38598800-38599400	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr17:38598800-38599400	Flanking Active TSS	Colon Smooth Muscle	Colon
28	chr17:38598800-38599400	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr17:38598800-38599400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr17:38598800-38599400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr17:38598800-38599400	Flanking Active TSS	K562	blood
32	chr17:38598800-38599400	Flanking Active TSS	NHLF	lung
33	chr17:38598800-38599400	Flanking Active TSS	Osteobl	bone
34	chr17:38598800-38599600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr17:38598800-38599600	Flanking Active TSS	Colonic Mucosa	Colon
36	chr17:38598800-38599600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
37	chr17:38598800-38599600	Flanking Active TSS	Dnd41	blood
38	chr17:38598800-38599800	Active TSS	Primary hematopoietic stem cells	blood
39	chr17:38598800-38600800	Active TSS	Brain Angular Gyrus	brain
40	chr17:38598800-38601400	Weak transcription	Hela-S3	cervix
41	chr17:38598800-38601800	Active TSS	H9 Cell Line	embryonic stem cell
42	chr17:38599000-38599200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr17:38599000-38599200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr17:38599000-38599200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr17:38599000-38599200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr17:38599000-38599200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr17:38599000-38599200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr17:38599000-38599200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr17:38599000-38599200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr17:38599000-38599200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood

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