Variant report

Variant	rs928781
Chromosome Location	chr22:23600013-23600014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:23571843..23573484-chr22:23598551..23600806,2	MCF-7	breast:
2	chr22:23599878..23601971-chr9:133779976..133781656,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11090228	0.91[CEU][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs11704376	0.82[CEU][hapmap]
rs11704598	0.83[CEU][hapmap]
rs11704766	0.83[CEU][hapmap]
rs11912657	0.83[CEU][hapmap];0.83[GIH][hapmap]
rs11912682	0.83[CEU][hapmap];0.83[GIH][hapmap]
rs11913665	0.85[CEU][hapmap]
rs12627853	0.83[ASN][1000 genomes]
rs13054840	0.82[CEU][hapmap]
rs16802	0.91[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs17611266	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1811017	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs1811018	0.80[EUR][1000 genomes]
rs2227939	0.88[EUR][1000 genomes]
rs2330369	0.83[CEU][hapmap]
rs3788358	0.95[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs5751619	0.88[EUR][1000 genomes]
rs5759665	0.82[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[LWK][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs5759666	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs5759675	0.82[CEU][hapmap]
rs5759679	0.84[CHB][hapmap];0.88[EUR][1000 genomes]
rs5759681	0.95[CEU][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs5759682	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs5759683	0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs5996507	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs5996508	0.88[EUR][1000 genomes]
rs6003584	0.82[AFR][1000 genomes]
rs6003586	0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs6003591	0.86[AMR][1000 genomes]
rs6003593	0.80[EUR][1000 genomes]
rs62219796	0.87[EUR][1000 genomes]
rs7289192	0.83[CEU][hapmap];0.81[GIH][hapmap]
rs7291469	0.83[CEU][hapmap];0.83[GIH][hapmap]
rs7292656	0.87[EUR][1000 genomes]
rs743584	0.83[CEU][hapmap];0.86[GIH][hapmap]
rs8139664	0.83[CEU][hapmap];0.83[GIH][hapmap]
rs928780	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9608091	0.86[AMR][1000 genomes]
rs9608093	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9608094	0.83[CEU][hapmap]
rs9608100	0.87[EUR][1000 genomes]
rs9612266	0.80[GIH][hapmap]
rs9612270	0.83[CEU][hapmap];0.86[GIH][hapmap]
rs9612275	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915235	chr22:22971768-23650987	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
2	esv3388845	chr22:22973346-23652447	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	100 gene(s)	inside rSNPs	diseases
3	nsv531799	chr22:22993679-23642142	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
4	nsv1061433	chr22:22997799-23649107	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
5	nsv521695	chr22:22998337-23648009	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
6	nsv915236	chr22:22998337-23650987	Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
7	nsv588512	chr22:22998337-23667731	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
8	nsv531800	chr22:23002708-23648163	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
9	nsv916593	chr22:23002709-23648790	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
10	nsv993496	chr22:23002709-23654222	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
11	nsv1067002	chr22:23007167-23643363	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
12	nsv1067324	chr22:23007367-23654223	Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
13	nsv533839	chr22:23012013-23643223	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
14	nsv916933	chr22:23012069-23654237	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
15	nsv531801	chr22:23028586-23657804	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	92 gene(s)	inside rSNPs	diseases
16	nsv531802	chr22:23046186-23627391	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	diseases
17	nsv1060509	chr22:23055148-23648719	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	83 gene(s)	inside rSNPs	diseases
18	nsv1056324	chr22:23055148-23750989	Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
19	nsv1062780	chr22:23060449-23648719	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
20	nsv948942	chr22:23063178-23645718	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
21	nsv1063200	chr22:23097177-23643224	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	80 gene(s)	inside rSNPs	diseases
22	nsv949250	chr22:23157485-23645718	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
23	nsv1057659	chr22:23400739-24138788	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
24	nsv588598	chr22:23530168-23638025	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
25	nsv9876	chr22:23563331-23923059	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
26	nsv482557	chr22:23584948-23741799	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
27	nsv531550	chr22:23589667-24012550	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
28	esv2762117	chr22:23592136-23996869	Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
29	nsv1063476	chr22:23596683-23989388	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
30	nsv544617	chr22:23596683-23989388	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
31	nsv1059951	chr22:23597270-23973060	Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs928781	BCR	cis	multi-tissue	Pritchard
rs928781	UBE2L3	cis	cerebellum	SCAN
rs928781	CABIN1	cis	cerebellum	SCAN
rs928781	BCR	cis	cerebellum	SCAN
rs928781	YPEL1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:23585800-23605600	Weak transcription	Fetal Lung	lung
2	chr22:23591000-23615800	Weak transcription	NH-A	brain
3	chr22:23591200-23604000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:23592800-23603800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr22:23593000-23618000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr22:23594400-23611800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr22:23594400-23614200	Weak transcription	A549	lung
8	chr22:23594800-23601000	Strong transcription	Primary T cells from cord blood	blood
9	chr22:23594800-23601600	Strong transcription	Primary hematopoietic stem cells	blood
10	chr22:23595000-23604600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr22:23595000-23610800	Strong transcription	K562	blood
12	chr22:23595000-23612200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr22:23595000-23612200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr22:23595000-23647000	Strong transcription	Dnd41	blood
15	chr22:23595200-23600600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr22:23595200-23623600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr22:23595400-23623800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr22:23595600-23607200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr22:23595600-23609200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr22:23595600-23619200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr22:23595600-23623600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr22:23595800-23600600	Strong transcription	Primary B cells from cord blood	blood
23	chr22:23595800-23601000	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr22:23595800-23601000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr22:23595800-23601200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr22:23595800-23601400	Strong transcription	Brain Germinal Matrix	brain
27	chr22:23595800-23601400	Strong transcription	Fetal Brain Female	brain
28	chr22:23595800-23601600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr22:23595800-23602400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr22:23595800-23608200	Strong transcription	Thymus	Thymus
31	chr22:23595800-23609000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr22:23595800-23611600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr22:23595800-23621000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr22:23595800-23623400	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr22:23595800-23649600	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr22:23596000-23600400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr22:23596000-23601000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr22:23596000-23604000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr22:23596000-23608200	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr22:23596800-23603200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr22:23597200-23603400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr22:23597400-23600400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr22:23597600-23600200	Genic enhancers	Fetal Intestine Small	intestine
44	chr22:23597600-23601400	Genic enhancers	Gastric	stomach
45	chr22:23597600-23601600	Genic enhancers	Spleen	Spleen
46	chr22:23597800-23600200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr22:23597800-23600400	Genic enhancers	Right Atrium	heart
48	chr22:23597800-23600600	Enhancers	Fetal Heart	heart
49	chr22:23597800-23600600	Enhancers	Stomach Mucosa	stomach
50	chr22:23597800-23600800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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