Variant report

Variant	rs17663045
Chromosome Location	chr2:20824691-20824692
allele	C/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	CTCF	chr2:20824680-20824830	WERI-Rb-1	eye:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20643596..20652981-chr2:20820571..20828990,20	MCF-7	breast:
2	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:

Variant related genes	Relation type
HS1BP3	TF binding region
ENSG00000228950	Chromatin interaction
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10495708	0.95[CEU][hapmap];0.88[CHB][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13003661	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[TSI][hapmap]
rs13027694	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17662465	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17662495	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17662614	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17662644	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17719096	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17719114	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17719159	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2305459	0.80[EUR][1000 genomes]
rs34101445	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34216303	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34405290	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35001606	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35264816	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35311387	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35404888	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35527388	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35755927	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3732150	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3732158	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4456661	1.00[CHB][hapmap]
rs4666441	0.95[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56905664	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60541580	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6531249	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67364128	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72782402	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs744663	0.80[EUR][1000 genomes]
rs745687	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs870309	0.88[CHB][hapmap]
rs896736	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9306893	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv581167	chr2:20791125-20827846	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1008473	chr2:20811359-20879186	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv535599	chr2:20811359-20879186	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv517472	chr2:20814583-20855176	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv873725	chr2:20814583-20855176	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	nsv527901	chr2:20818458-20876386	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17663045	WDR35	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20815000-20831800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:20815000-20847600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:20817200-20826600	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:20817400-20827200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:20817400-20831400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:20817400-20835200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:20817400-20847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:20817600-20832200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:20817600-20850000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:20817800-20826200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:20817800-20833800	Weak transcription	Fetal Thymus	thymus
12	chr2:20818000-20825600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:20818200-20825200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:20818200-20828600	Weak transcription	Fetal Kidney	kidney
15	chr2:20818200-20835000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:20818200-20835000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr2:20818400-20825000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr2:20818400-20825600	Weak transcription	HUVEC	blood vessel
19	chr2:20818400-20828800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:20818400-20828800	Weak transcription	Fetal Brain Male	brain
21	chr2:20818400-20831800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:20818600-20824800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr2:20818600-20825600	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:20818800-20824800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:20818800-20825200	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:20818800-20826200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
27	chr2:20818800-20833600	Weak transcription	A549	lung
28	chr2:20818800-20842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr2:20819000-20847400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:20819200-20825000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:20819200-20825400	Strong transcription	Primary B cells from cord blood	blood
32	chr2:20819200-20826200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr2:20819200-20827000	Strong transcription	Primary T cells from cord blood	blood
34	chr2:20819200-20827200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:20819400-20824800	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr2:20819400-20825000	Strong transcription	NHLF	lung
37	chr2:20819400-20825600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:20819400-20834200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:20819400-20847800	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr2:20819600-20825000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr2:20819600-20825200	Strong transcription	Colonic Mucosa	Colon
42	chr2:20819600-20825200	Genic enhancers	Fetal Muscle Leg	muscle
43	chr2:20819600-20825600	Strong transcription	Pancreas	Pancrea
44	chr2:20819800-20825200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:20819800-20826400	Strong transcription	Aorta	Aorta
46	chr2:20819800-20826800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr2:20819800-20834200	Weak transcription	Osteobl	bone
48	chr2:20820000-20824800	Strong transcription	Ovary	ovary
49	chr2:20820400-20825000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:20820600-20826000	Strong transcription	Fetal Stomach	stomach

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