Variant report

Variant	rs12221474
Chromosome Location	chr10:99332488-99332489
allele	A/C
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	TCF12	chr10:99331350-99332874	ECC-1	luminal epithelium:	n/a	chr10:99331620-99331627
2	CTCF	chr10:99331468-99332640	A549	lung:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
3	RAD21	chr10:99331848-99332601	ECC-1	luminal epithelium:	n/a	chr10:99332173-99332192 chr10:99332322-99332334 chr10:99332178-99332190
4	RAD21	chr10:99331316-99332653	HCT-116	colon:	n/a	chr10:99332173-99332192 chr10:99332322-99332334 chr10:99332178-99332190
5	NFIC	chr10:99331852-99332588	ECC-1	luminal epithelium:	n/a	chr10:99332241-99332258 chr10:99332241-99332257
6	RAD21	chr10:99331701-99332588	A549	lung:	n/a	chr10:99332173-99332192 chr10:99332322-99332334 chr10:99332178-99332190
7	HMGN3	chr10:99332062-99332515	K562	blood:	n/a	n/a
8	CTCF	chr10:99332432-99332491	GM19240	blood:	n/a	n/a
9	MAX	chr10:99331959-99332537	ECC-1	luminal epithelium:	n/a	chr10:99332237-99332246
10	NFIC	chr10:99331937-99332627	SK-N-SH	brain:	n/a	chr10:99332241-99332258 chr10:99332241-99332257
11	TCF12	chr10:99331890-99332575	A549	lung:	n/a	n/a
12	SPI1	chr10:99331903-99332584	GM12878	blood:	n/a	n/a
13	CTCF	chr10:99331894-99332489	MCF-7	breast:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
14	SIN3AK20	chr10:99330999-99332539	MCF-7	breast:	n/a	n/a
15	SMC3	chr10:99330257-99333212	SK-N-SH	brain:	n/a	chr10:99331517-99331524 chr10:99332174-99332188
16	CTCF	chr10:99332420-99332570	HAc	cerebellar:	n/a	n/a
17	RAD21	chr10:99331252-99332569	HCT-116	colon:	n/a	chr10:99332173-99332192 chr10:99332322-99332334 chr10:99332178-99332190
18	RAD21	chr10:99331646-99332506	H1-hESC	embryonic stem cell:	n/a	chr10:99332173-99332192 chr10:99332322-99332334 chr10:99332178-99332190
19	MAX	chr10:99331765-99333272	A549	lung:	n/a	chr10:99333159-99333169 chr10:99332237-99332246
20	CTCF	chr10:99331554-99332550	SK-N-SH	brain:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
21	CTCF	chr10:99331324-99332695	HCT-116	colon:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
22	CEBPB	chr10:99331903-99332575	A549	lung:	n/a	n/a
23	MAX	chr10:99331928-99332652	A549	lung:	n/a	chr10:99332237-99332246

No.	Distal block	Cell Line	Cell type
1	chr10:99255590..99258774-chr10:99331777..99334688,4	MCF-7	breast:
2	chr10:99332396..99334042-chr10:99392626..99394470,2	K562	blood:
3	chr10:99222708..99225169-chr10:99331581..99333239,2	MCF-7	breast:
4	chr10:99329733..99337149-chr10:99338392..99346753,19	MCF-7	breast:
5	chr10:99256533..99260506-chr10:99329939..99335950,10	MCF-7	breast:
6	chr10:99205743..99208350-chr10:99330121..99333769,3	MCF-7	breast:

Variant related genes	Relation type
ANKRD2	TF binding region
ENSG00000155229	Chromatin interaction
ENSG00000241935	Chromatin interaction
ENSG00000171307	Chromatin interaction
ENSG00000171160	Chromatin interaction
ENSG00000165886	Chromatin interaction
ENSG00000171311	Chromatin interaction
ENSG00000249967	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10748698	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10748699	0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.89[ASN][1000 genomes]
rs10748700	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10882956	0.81[ASN][1000 genomes]
rs10882959	0.93[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10882961	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10882962	0.93[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882963	0.94[CEU][hapmap];0.83[GIH][hapmap]
rs10882965	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10882966	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11189244	0.82[MEX][hapmap]
rs11189259	0.88[MEX][hapmap]
rs11189266	0.81[ASN][1000 genomes]
rs11189274	0.89[CEU][hapmap]
rs11189275	0.92[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11189278	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11189280	0.82[EUR][1000 genomes]
rs11189284	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs11528108	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11528109	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11814566	0.84[CEU][hapmap]
rs12219064	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12243136	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12357750	0.84[EUR][1000 genomes]
rs1417408	0.89[CEU][hapmap]
rs1475757	0.83[ASN][1000 genomes]
rs1572860	0.93[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17108059	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3814554	0.89[CEU][hapmap]
rs3818910	0.95[CEU][hapmap]
rs4635019	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4919104	0.94[MEX][hapmap]
rs7077211	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7094973	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7475470	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7893335	0.82[MEX][hapmap]
rs7902642	1.00[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7921278	0.81[ASN][1000 genomes]
rs7921505	0.81[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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS 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	66 gene(s)	inside rSNPs	diseases
2	nsv1036494	chr10:99267639-99345207	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv1047359	chr10:99306501-99369013	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12221474	RRP12	cis	parietal	SCAN
rs12221474	C10orf28	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99321200-99334600	Weak transcription	HepG2	liver
2	chr10:99322000-99333000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr10:99325600-99334600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr10:99326000-99334200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr10:99326400-99334200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr10:99327000-99334600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr10:99327200-99334600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr10:99327800-99334400	Weak transcription	Colon Smooth Muscle	Colon
9	chr10:99329200-99334000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr10:99329600-99334600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr10:99329800-99333000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr10:99329800-99333000	Enhancers	Esophagus	oesophagus
13	chr10:99329800-99336000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr10:99330000-99335400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr10:99330400-99332600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr10:99330600-99332600	Enhancers	Brain Hippocampus Middle	brain
17	chr10:99330800-99334200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:99330800-99334400	Weak transcription	NHLF	lung
19	chr10:99330800-99334600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr10:99330800-99335000	Weak transcription	Ovary	ovary
21	chr10:99330800-99335400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr10:99330800-99336200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr10:99330800-99336200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr10:99330800-99336200	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr10:99331000-99332600	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr10:99331000-99332600	Enhancers	Stomach Mucosa	stomach
27	chr10:99331000-99337200	Enhancers	Fetal Heart	heart
28	chr10:99331200-99332600	Enhancers	Fetal Intestine Small	intestine
29	chr10:99331200-99332800	Enhancers	Brain Anterior Caudate	brain
30	chr10:99331200-99332800	Enhancers	Gastric	stomach
31	chr10:99331200-99333000	Enhancers	Placenta	Placenta
32	chr10:99331200-99334400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr10:99331200-99334400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr10:99331400-99332600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr10:99331400-99333200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr10:99331400-99336000	Enhancers	Fetal Muscle Leg	muscle
37	chr10:99331400-99336200	Enhancers	Hela-S3	cervix
38	chr10:99331600-99332600	Enhancers	Brain Cingulate Gyrus	brain
39	chr10:99331600-99332600	Genic enhancers	Lung	lung
40	chr10:99331600-99333400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr10:99331800-99332600	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr10:99331800-99332600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr10:99331800-99332800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr10:99331800-99332800	Enhancers	Adipose Nuclei	Adipose
45	chr10:99331800-99332800	Enhancers	Liver	Liver
46	chr10:99331800-99332800	Enhancers	Brain Substantia Nigra	brain
47	chr10:99331800-99334200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr10:99331800-99334400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr10:99331800-99334800	Enhancers	Stomach Smooth Muscle	stomach
50	chr10:99332000-99332800	Enhancers	Pancreas	Pancrea

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