Variant report

Variant	rs5749631
Chromosome Location	chr22:33965006-33965007
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	RCOR1	chr22:33964922-33965472	GM12878	blood:	n/a	n/a
2	ZNF384	chr22:33964086-33965213	GM12878	blood:	n/a	n/a
3	CTCF	chr22:33964900-33965050	GM12873	blood:	n/a	n/a
4	RUNX3	chr22:33963880-33965234	GM12878	blood:	n/a	n/a
5	WRNIP1	chr22:33964938-33965083	GM12878	blood:	n/a	n/a
6	IKZF1	chr22:33964018-33965167	GM12878	blood:	n/a	n/a
7	RUNX3	chr22:33963911-33965177	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:33964224..33966733-chr22:33974082..33975978,2	MCF-7	breast:

Variant related genes	Relation type
LARGE	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1547070	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[ASN][1000 genomes]
rs1972208	0.84[ASN][1000 genomes]
rs2027834	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2065048	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2105852	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2283918	0.88[ASN][1000 genomes]
rs2413191	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2413192	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs2413193	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs28703205	0.83[ASN][1000 genomes]
rs2899210	1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs3819663	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4821163	0.84[ASN][1000 genomes]
rs4821164	0.84[ASN][1000 genomes]
rs4821166	0.90[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs5749627	1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[ASN][1000 genomes]
rs5754609	0.93[ASN][1000 genomes]
rs5754611	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs5754612	0.85[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs713703	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs713795	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs743728	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs762057	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[ASN][1000 genomes]
rs762058	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[ASN][1000 genomes]
rs762059	0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs762060	0.91[ASN][1000 genomes]
rs762062	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs9609818	0.82[ASN][1000 genomes]
rs9609819	0.84[ASN][1000 genomes]
rs9609824	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs989557	1.00[CHB][hapmap];0.86[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1062127	chr22:33755479-34085278	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544683	chr22:33755479-34085278	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv531588	chr22:33776857-34150188	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv914983	chr22:33800119-34035034	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1060283	chr22:33809137-34043739	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv544684	chr22:33809137-34043739	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1055791	chr22:33822226-34159536	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1065417	chr22:33823850-34053325	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
11	nsv933309	chr22:33825232-34053000	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
12	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
13	nsv917167	chr22:33852676-34137036	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1062832	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv544686	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv914986	chr22:33863218-33967289	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv914987	chr22:33920421-34047427	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
19	nsv1063312	chr22:33963672-33983973	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv588933	chr22:33963790-33978458	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5749631	KREMEN1	cis	cerebellum	SCAN
rs5749631	YWHAH	cis	cerebellum	SCAN
rs5749631	ZNRF3	cis	cerebellum	SCAN
rs5749631	LARGE	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33917400-33966800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr22:33939800-33965200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr22:33940800-33970600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr22:33946000-33974600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr22:33949400-33965200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr22:33949600-33975400	Weak transcription	Ovary	ovary
7	chr22:33952400-33969400	Weak transcription	A549	lung
8	chr22:33958400-33967000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr22:33959000-33965200	Weak transcription	Brain Hippocampus Middle	brain
10	chr22:33959200-33966800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr22:33959400-33974800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr22:33960000-33966000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr22:33960000-33993000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr22:33960400-33969200	Weak transcription	Fetal Intestine Large	intestine
15	chr22:33961000-33969200	Weak transcription	Fetal Intestine Small	intestine
16	chr22:33961200-33965400	Weak transcription	Liver	Liver
17	chr22:33962600-33967400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr22:33963000-33965600	Weak transcription	Small Intestine	intestine
19	chr22:33963400-33966200	Enhancers	Fetal Kidney	kidney
20	chr22:33963600-33966400	Enhancers	Right Ventricle	heart
21	chr22:33963800-33965200	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr22:33963800-33966200	Enhancers	Fetal Heart	heart
23	chr22:33963800-33966600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr22:33964000-33965200	Enhancers	Pancreas	Pancrea
25	chr22:33964000-33965600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr22:33964000-33965800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr22:33964000-33966200	Enhancers	Primary hematopoietic stem cells	blood
28	chr22:33964000-33966200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr22:33964000-33966200	Enhancers	Left Ventricle	heart
30	chr22:33964000-33966200	Enhancers	HepG2	liver
31	chr22:33964000-33966400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr22:33964000-33966400	Enhancers	Spleen	Spleen
33	chr22:33964200-33965400	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr22:33964200-33965800	Enhancers	Adipose Nuclei	Adipose
35	chr22:33964200-33965800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr22:33964200-33966000	Enhancers	Right Atrium	heart
37	chr22:33964600-33966200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr22:33964600-33966400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr22:33964800-33965200	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr22:33964800-33965200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr22:33964800-33965200	Enhancers	Stomach Smooth Muscle	stomach
42	chr22:33964800-33965400	Enhancers	Colon Smooth Muscle	Colon
43	chr22:33964800-33965400	Flanking Active TSS	GM12878-XiMat	blood
44	chr22:33964800-33965600	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr22:33964800-33965600	Enhancers	Rectal Smooth Muscle	rectum
46	chr22:33964800-33965800	Enhancers	Brain Germinal Matrix	brain
47	chr22:33964800-33965800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr22:33964800-33966000	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr22:33964800-33966200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr22:33964800-33966200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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