Variant report

Variant	rs721933
Chromosome Location	chr2:20190683-20190684
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	chr2:20188774-20190793	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr2:20188716-20190757	A549	lung:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
3	TCF12	chr2:20188950-20190739	A549	lung:	n/a	n/a
4	HEY1	chr2:20189555-20190707	HepG2	liver:	n/a	n/a
5	MBD4	chr2:20189275-20190770	HepG2	liver:	n/a	n/a
6	GATA3	chr2:20190349-20190762	SH-SY5Y	brain:	n/a	n/a
7	POLR2A	chr2:20189602-20191288	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:20189522-20190804	HepG2	liver:	n/a	n/a
9	HCFC1	chr2:20188796-20191052	Hela-S3	cervix:	n/a	n/a
10	MXI1	chr2:20187611-20190928	SK-N-SH	brain:	n/a	chr2:20189876-20189891 chr2:20189874-20189889

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20099026..20101634-chr2:20189872..20192427,2	K562	blood:
2	chr2:20188544..20190994-chr2:20211302..20213941,2	MCF-7	breast:

Variant related genes	Relation type
WDR35	TF binding region
ENSG00000132031	Chromatin interaction
ENSG00000183891	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1056233	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1115275	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11680554	0.88[CEU][hapmap];0.87[AMR][1000 genomes]
rs11681705	0.90[ASW][hapmap];0.94[CEU][hapmap];0.89[GIH][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11683973	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11688098	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11688680	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11693384	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11694821	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11896116	0.88[CHD][hapmap]
rs12986437	0.94[CEU][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12988913	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12990087	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12995324	0.81[AMR][1000 genomes]
rs12996974	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13001254	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13005512	0.88[CEU][hapmap];0.87[AMR][1000 genomes]
rs13006748	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13011870	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13035048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1370585	0.90[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16987220	0.94[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16987257	1.00[ASW][hapmap];0.94[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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17695872	0.88[CEU][hapmap];0.92[GIH][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1921731	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1992167	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2028208	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];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28452699	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34400777	1.00[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34425205	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34459327	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34595677	0.81[AMR][1000 genomes]
rs34741640	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35307726	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35425971	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35973216	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4294960	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66496755	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6706311	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6720011	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67653248	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67724270	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67915887	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs721932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73214266	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs957614	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][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	nsv1006404	chr2:20167688-20216509	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1005431	chr2:20174676-20210163	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1011244	chr2:20174676-20216204	Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs721933	WDR35	cis	parietal	SCAN
rs721933	TTC32	cis	lymphoblastoid	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20188600-20190800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr2:20188800-20190800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:20188800-20190800	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr2:20189000-20190800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:20189200-20190800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr2:20189200-20190800	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr2:20189200-20191000	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr2:20189800-20190800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:20190200-20190800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:20190200-20190800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:20190200-20190800	Flanking Active TSS	Brain Angular Gyrus	brain
12	chr2:20190400-20190800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:20190400-20190800	Enhancers	Fetal Heart	heart
14	chr2:20190400-20190800	Flanking Active TSS	A549	lung
15	chr2:20190400-20190800	Flanking Active TSS	NHEK	skin
16	chr2:20190400-20191000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr2:20190400-20191000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr2:20190400-20191400	Flanking Active TSS	HepG2	liver
19	chr2:20190400-20194600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:20190400-20207400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:20190600-20190800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr2:20190600-20190800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:20190600-20190800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:20190600-20190800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr2:20190600-20190800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr2:20190600-20190800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
27	chr2:20190600-20190800	Bivalent Enhancer	Primary B cells from cord blood	blood
28	chr2:20190600-20190800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
29	chr2:20190600-20190800	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr2:20190600-20190800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:20190600-20190800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:20190600-20190800	Enhancers	Brain Substantia Nigra	brain
33	chr2:20190600-20190800	Bivalent/Poised TSS	Fetal Brain Male	brain
34	chr2:20190600-20190800	Enhancers	Fetal Intestine Small	intestine
35	chr2:20190600-20190800	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr2:20190600-20190800	Flanking Active TSS	HMEC	breast
37	chr2:20190600-20191000	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr2:20190600-20191200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:20190600-20192800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:20190600-20193200	Weak transcription	Fetal Lung	lung
41	chr2:20190600-20201000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:20190600-20211400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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