Variant report

Variant	rs2227589
Chromosome Location	chr1:173886216-173886217
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	POLR2A	chr1:173886085-173886860	HepG2	liver:	n/a	n/a
2	MAX	chr1:173886170-173887715	HepG2	liver:	n/a	chr1:173886747-173886756
3	RCOR1	chr1:173886085-173886719	HepG2	liver:	n/a	n/a
4	NFIC	chr1:173885997-173886763	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:173886215-173886913	HepG2	liver:	n/a	n/a
6	MAZ	chr1:173886085-173886658	K562	blood:	n/a	n/a
7	MYBL2	chr1:173886170-173886877	HepG2	liver:	n/a	n/a
8	HNF4A	chr1:173886213-173886754	HepG2	liver:	n/a	chr1:173886539-173886554 chr1:173886539-173886553 chr1:173886612-173886625 chr1:173886537-173886549 chr1:173886539-173886553 chr1:173886539-173886552 chr1:173886612-173886625
9	POLR2A	chr1:173885847-173886897	HepG2	liver:	n/a	n/a
10	GATA1	chr1:173885144-173886920	K562	blood:	n/a	chr1:173885345-173885352 chr1:173885345-173885352 chr1:173885345-173885352 chr1:173885338-173885359
11	MYBL2	chr1:173885987-173886859	HepG2	liver:	n/a	n/a
12	CHD2	chr1:173886049-173886844	HepG2	liver:	n/a	n/a
13	POLR2A	chr1:173886150-173886818	HepG2	liver:	n/a	n/a
14	RCOR1	chr1:173886087-173886642	K562	blood:	n/a	n/a
15	RXRA	chr1:173886190-173886867	HepG2	liver:	n/a	chr1:173886539-173886552 chr1:173886539-173886552 chr1:173886536-173886556
16	HEY1	chr1:173886169-173886924	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:173882932..173886692-chr1:173886862..173890895,4	K562	blood:
2	chr1:173837862..173839508-chr1:173885268..173887307,2	MCF-7	breast:
3	chr1:173829871..173833250-chr1:173884943..173888028,3	K562	blood:
4	chr1:173832421..173839801-chr1:173885332..173891780,9	MCF-7	breast:

Variant related genes	Relation type
RNA5SP67	TF binding region
SERPINC1	TF binding region
ENSG00000234741	Chromatin interaction
ENSG00000208317	Chromatin interaction
ENSG00000252231	Chromatin interaction
ENSG00000270084	Chromatin interaction
ENSG00000185278	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs16846418	0.83[EUR][1000 genomes]
rs16846433	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16846478	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16846526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16846546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16846561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16846593	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2065170	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2068871	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2146372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2227592	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[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]
rs2235095	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2759328	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3791021	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3791022	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs57022387	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58994962	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59393482	0.88[AMR][1000 genomes]
rs60689957	0.88[AMR][1000 genomes]
rs61262741	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6656255	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6685043	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6691053	0.82[CHB][hapmap]
rs6696381	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6790	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7521960	0.83[AFR][1000 genomes]
rs941987	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs941988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[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];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9970048	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2227589		cis	Lymphoblastoid	GTEx
rs2227589	SNORD78	cis	parietal	SCAN
rs2227589	PRDX6	cis	parietal	SCAN
rs2227589	SNORD79	cis	parietal	SCAN
rs2227589	dJ383J4.3	cis	multi-tissue	Pritchard
rs2227589	CENPL	cis	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173856600-173907200	Weak transcription	Brain Germinal Matrix	brain
2	chr1:173857400-173902000	Weak transcription	HSMMtube	muscle
3	chr1:173858200-173902800	Weak transcription	Left Ventricle	heart
4	chr1:173858600-173886800	Weak transcription	Placenta	Placenta
5	chr1:173862000-173891600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:173864600-173886600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:173870000-173898000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:173870400-173887400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:173871200-173908400	Weak transcription	Spleen	Spleen
10	chr1:173872400-173896200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:173874400-173899800	Weak transcription	Primary T cells from cord blood	blood
12	chr1:173879200-173899400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:173882800-173912400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:173883800-173887200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:173884400-173886800	Active TSS	Liver	Liver
16	chr1:173885400-173887400	Enhancers	Fetal Intestine Small	intestine
17	chr1:173885400-173887400	Enhancers	K562	blood
18	chr1:173885800-173887000	Enhancers	Fetal Intestine Large	intestine
19	chr1:173886000-173886600	Active TSS	HepG2	liver

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