Variant report

Variant	rs3814554
Chromosome Location	chr10:99331201-99331202
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	ELF1	chr10:99331098-99331888	MCF-7	breast:	n/a	n/a
2	NR2F2	chr10:99331136-99331851	MCF-7	breast:	n/a	n/a
3	TCF12	chr10:99331089-99332118	MCF-7	breast:	n/a	chr10:99331121-99331131 chr10:99331620-99331627
4	RAD21	chr10:99330390-99332450	SK-N-SH	brain:	n/a	chr10:99332173-99332192 chr10:99332322-99332334 chr10:99332178-99332190
5	EP300	chr10:99331192-99331885	MCF-7	breast:	n/a	chr10:99331421-99331435 chr10:99331315-99331322
6	SIN3AK20	chr10:99330999-99332539	MCF-7	breast:	n/a	n/a
7	NR2F2	chr10:99331147-99331883	MCF-7	breast:	n/a	n/a
8	SMC3	chr10:99330257-99333212	SK-N-SH	brain:	n/a	chr10:99331517-99331524 chr10:99332174-99332188
9	CTCF	chr10:99331160-99331310	GM12864	blood:	n/a	n/a
10	ELF1	chr10:99331113-99332449	MCF-7	breast:	n/a	n/a
11	HDAC2	chr10:99331164-99331862	MCF-7	breast:	n/a	n/a
12	GATA3	chr10:99331146-99331840	MCF-7	breast:	n/a	n/a
13	EP300	chr10:99331156-99331880	MCF-7	breast:	n/a	chr10:99331421-99331435 chr10:99331315-99331322
14	MAX	chr10:99331186-99331824	MCF-7	breast:	n/a	n/a
15	GATA3	chr10:99331054-99331970	MCF-7	breast:	n/a	n/a
16	SIN3AK20	chr10:99331113-99331905	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:99326572..99328961-chr10:99329833..99332100,2	K562	blood:
2	chr10:99331048..99332027-chr10:99339659..99340637,7	MCF-7	breast:
3	chr10:99328694..99331523-chr10:99333360..99336351,3	MCF-7	breast:
4	chr10:99331139..99331795-chr10:99344716..99345483,2	MCF-7	breast:
5	chr10:99330995..99332069-chr10:99339678..99340684,16	MCF-7	breast:
6	chr10:99330373..99332190-chr5:177631537..177633145,2	MCF-7	breast:
7	chr10:99329733..99337149-chr10:99338392..99346753,19	MCF-7	breast:
8	chr10:99331112..99332069-chr10:99339738..99340684,9	MCF-7	breast:
9	chr10:99256533..99260506-chr10:99329939..99335950,10	MCF-7	breast:
10	chr10:99311940..99314624-chr10:99329998..99332096,2	MCF-7	breast:
11	chr10:99205743..99208350-chr10:99330121..99333769,3	MCF-7	breast:

Variant related genes	Relation type
ANKRD2	TF binding region
ENSG00000165886	Chromatin interaction
ENSG00000197451	Chromatin interaction
ENSG00000171311	Chromatin interaction
ENSG00000155229	Chromatin interaction
ENSG00000249967	Chromatin interaction
ENSG00000241935	Chromatin interaction
ENSG00000171307	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1018727	0.80[EUR][1000 genomes]
rs10748699	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs10748700	0.81[EUR][1000 genomes]
rs10882957	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10882959	0.95[CEU][hapmap]
rs10882961	0.81[EUR][1000 genomes]
rs10882962	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs10882963	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10882965	0.83[EUR][1000 genomes]
rs10882966	0.81[EUR][1000 genomes]
rs10882967	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1107517	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1107518	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11189267	0.87[ASN][1000 genomes]
rs11189270	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11189274	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11189275	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs11189278	0.83[EUR][1000 genomes]
rs11189280	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189284	0.86[CEU][hapmap];0.87[ASN][1000 genomes]
rs11511362	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11528108	0.84[EUR][1000 genomes]
rs11528109	0.84[EUR][1000 genomes]
rs11814566	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12219064	0.90[CEU][hapmap]
rs12221474	0.89[CEU][hapmap]
rs12243136	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12355384	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12357750	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12415338	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12766074	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12767760	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12774288	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12775868	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12783481	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1417408	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1475757	0.84[EUR][1000 genomes]
rs1572860	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs17108059	0.82[EUR][1000 genomes]
rs3818910	0.86[CEU][hapmap]
rs4244325	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4244326	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4635019	0.83[EUR][1000 genomes]
rs4919108	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4919109	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66521603	0.82[ASN][1000 genomes]
rs68084394	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7077211	0.84[EUR][1000 genomes]
rs7077976	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7094973	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7342022	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7475470	0.83[EUR][1000 genomes]
rs7475851	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7902642	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7908668	0.86[EUR][1000 genomes]
rs7911122	0.80[AMR][1000 genomes];0.92[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

No data

Chromatin state (count:86 , 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	chr10:99325400-99332200	Weak transcription	HUVEC	blood vessel
4	chr10:99325600-99334600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr10:99326000-99332200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr10:99326000-99334200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr10:99326400-99334200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr10:99327000-99334600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr10:99327200-99332200	Weak transcription	Right Atrium	heart
10	chr10:99327200-99334600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr10:99327600-99331400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr10:99327600-99331400	Strong transcription	Stomach Smooth Muscle	stomach
13	chr10:99327600-99331600	Strong transcription	Lung	lung
14	chr10:99327600-99332200	Strong transcription	Spleen	Spleen
15	chr10:99327600-99332400	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr10:99327800-99331400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr10:99327800-99331400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr10:99327800-99331400	Strong transcription	Right Ventricle	heart
19	chr10:99327800-99331600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr10:99327800-99331600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr10:99327800-99331800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr10:99327800-99331800	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr10:99327800-99331800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr10:99327800-99331800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr10:99327800-99332000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr10:99327800-99332000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr10:99327800-99334400	Weak transcription	Colon Smooth Muscle	Colon
28	chr10:99328000-99331600	Strong transcription	Liver	Liver
29	chr10:99328000-99332000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr10:99328800-99331400	Genic enhancers	Fetal Muscle Leg	muscle
31	chr10:99328800-99331800	Strong transcription	Fetal Stomach	stomach
32	chr10:99329000-99331400	Strong transcription	Osteobl	bone
33	chr10:99329200-99331400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr10:99329200-99331800	Genic enhancers	Fetal Muscle Trunk	muscle
35	chr10:99329200-99332200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr10:99329200-99334000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr10:99329600-99331400	Weak transcription	NH-A	brain
38	chr10:99329600-99332200	Weak transcription	NHDF-Ad	bronchial
39	chr10:99329600-99334600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr10:99329800-99331400	Enhancers	HSMM	muscle
41	chr10:99329800-99331600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr10:99329800-99333000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr10:99329800-99333000	Enhancers	Esophagus	oesophagus
44	chr10:99329800-99336000	Enhancers	Placenta Amnion	Placenta Amnion
45	chr10:99330000-99331800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr10:99330000-99335400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr10:99330200-99331600	Genic enhancers	Brain Cingulate Gyrus	brain
48	chr10:99330200-99332400	Enhancers	HSMMtube	muscle
49	chr10:99330400-99332600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr10:99330600-99331600	Enhancers	A549	lung

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