Variant report

Variant	rs165649
Chromosome Location	chr22:29874250-29874251
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	BACH1	chr22:29873931-29874298	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr22:29873916-29875515	U87	brain:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
3	REST	chr22:29873863-29875121	SK-N-SH	brain:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
4	REST	chr22:29873986-29875289	H1-hESC	embryonic stem cell:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
5	ZNF263	chr22:29873981-29874341	HEK293-T-REx	kidney:	n/a	chr22:29874137-29874146 chr22:29874139-29874160
6	REST	chr22:29873896-29875162	PFSK-1	brain:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
7	REST	chr22:29874019-29875106	PANC-1	pancreas:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
8	REST	chr22:29873775-29875378	PFSK-1	brain:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
9	REST	chr22:29873919-29875187	K562	blood:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
10	REST	chr22:29874169-29875048	GM12878	blood:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
11	MAZ	chr22:29873999-29874868	K562	blood:	n/a	chr22:29874642-29874651
12	ZNF143	chr22:29874014-29874267	H1-hESC	embryonic stem cell:	n/a	n/a
13	REST	chr22:29874144-29875236	HL-60	blood:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
14	REST	chr22:29874044-29874325	H1-hESC	embryonic stem cell:	n/a	chr22:29874180-29874189
15	REST	chr22:29874237-29875091	PFSK-1	brain:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684
16	REST	chr22:29873719-29876257	ECC-1	luminal epithelium:	n/a	chr22:29874670-29874684 chr22:29876114-29876127 chr22:29874664-29874684 chr22:29876194-29876204 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189 chr22:29876192-29876206
17	REST	chr22:29873870-29875517	U87	brain:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
18	REST	chr22:29873746-29875512	A549	lung:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
19	BACH1	chr22:29873953-29874359	K562	blood:	n/a	n/a
20	REST	chr22:29874047-29875214	MCF-7	breast:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
21	REST	chr22:29874078-29875227	PANC-1	pancreas:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
22	MXI1	chr22:29873451-29875094	SK-N-SH	brain:	n/a	n/a
23	REST	chr22:29873747-29876490	ECC-1	luminal epithelium:	n/a	chr22:29874670-29874684 chr22:29876114-29876127 chr22:29874664-29874684 chr22:29876194-29876204 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189 chr22:29876192-29876206
24	REST	chr22:29873788-29876008	HL-60	blood:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
25	MAFK	chr22:29873938-29874277	K562	blood:	n/a	chr22:29874127-29874142
26	REST	chr22:29874172-29875120	A549	lung:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
27	REST	chr22:29874063-29875122	MCF-7	breast:	n/a	chr22:29874670-29874684 chr22:29874664-29874684 chr22:29874664-29874673 chr22:29874667-29874680 chr22:29874672-29874682 chr22:29874664-29874684 chr22:29874665-29874683 chr22:29874664-29874684 chr22:29874180-29874189
28	MAFK	chr22:29873961-29874255	H1-hESC	embryonic stem cell:	n/a	chr22:29874127-29874142

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29702481..29704174-chr22:29874105..29876353,2	K562	blood:
2	chr22:29873715..29877046-chr22:29940798..29944268,3	K562	blood:

Variant related genes	Relation type
NEFH	TF binding region
RFPL1S	TF binding region
ENSG00000100296	Chromatin interaction
ENSG00000185340	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs105268	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs165602	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs165607	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs165624	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs165633	1.00[ASW][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.85[MKK][hapmap]
rs165697	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs165734	1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs165821	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs165823	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs165853	0.91[AMR][1000 genomes]
rs165899	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs174649	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174718	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs174721	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs174722	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2008880	1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[AMR][1000 genomes]
rs2857634	1.00[JPT][hapmap]
rs424541	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447914	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs457930	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs465736	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs467669	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs467768	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs4823046	1.00[JPT][hapmap]
rs5752916	1.00[CEU][hapmap]
rs5752917	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs5763238	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5763247	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5763315	1.00[JPT][hapmap]
rs5763347	1.00[JPT][hapmap]
rs5763348	1.00[JPT][hapmap]
rs6006219	1.00[JPT][hapmap]
rs737979	1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs9306464	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9608766	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9613908	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9613915	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9613919	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[ASN][1000 genomes]

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	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised 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	19 gene(s)	inside rSNPs	diseases
4	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer 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
7	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS 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 miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv1062039	chr22:29854861-29889201	Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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
10	nsv438344	chr22:29856079-29886043	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs165649	TPST2	cis	cerebellum	SCAN
rs165649	C22orf13	cis	parietal	SCAN
rs165649	RNF185	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29871600-29874400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr22:29873200-29875400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr22:29873400-29874400	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr22:29873400-29875800	Enhancers	K562	blood
5	chr22:29873600-29874400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
6	chr22:29873600-29874800	Enhancers	Brain Substantia Nigra	brain
7	chr22:29873600-29874800	Flanking Active TSS	Fetal Brain Female	brain
8	chr22:29873600-29875000	Enhancers	Dnd41	blood
9	chr22:29873600-29875600	Enhancers	Fetal Brain Male	brain
10	chr22:29873800-29874400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr22:29873800-29874600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr22:29873800-29874600	Flanking Active TSS	Brain Anterior Caudate	brain
13	chr22:29873800-29874600	Flanking Active TSS	A549	lung
14	chr22:29873800-29874600	Bivalent Enhancer	HSMMtube	muscle
15	chr22:29873800-29874800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:29873800-29875600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr22:29873800-29875800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
18	chr22:29873800-29876200	Bivalent Enhancer	Adipose Nuclei	Adipose
19	chr22:29873800-29876400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr22:29873800-29877800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
21	chr22:29873800-29877800	Bivalent Enhancer	Placenta	Placenta
22	chr22:29874000-29874400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
23	chr22:29874000-29874400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
24	chr22:29874000-29874400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
25	chr22:29874000-29874600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
26	chr22:29874000-29874600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr22:29874000-29874800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr22:29874000-29875200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr22:29874000-29876200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr22:29874200-29874400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
31	chr22:29874200-29874400	Enhancers	Primary hematopoietic stem cells	blood
32	chr22:29874200-29874400	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
33	chr22:29874200-29874400	Bivalent Enhancer	Left Ventricle	heart
34	chr22:29874200-29874400	Flanking Active TSS	Spleen	Spleen
35	chr22:29874200-29874400	Enhancers	HSMM	muscle
36	chr22:29874200-29874600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr22:29874200-29874600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
38	chr22:29874200-29874600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr22:29874200-29874600	Flanking Bivalent TSS/Enh	Brain Angular Gyrus	brain
40	chr22:29874200-29874800	Active TSS	H9 Cell Line	embryonic stem cell
41	chr22:29874200-29874800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr22:29874200-29875000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr22:29874200-29875200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
44	chr22:29874200-29875800	Enhancers	Ovary	ovary
45	chr22:29874200-29876000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
46	chr22:29874200-29876400	Bivalent Enhancer	Fetal Stomach	stomach

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