Variant report

Variant	rs74106638
Chromosome Location	chr1:97560219-97560220
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	TEAD4	chr1:97559544-97560544	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:97559313-97560306	PFSK-1	brain:	n/a	n/a
3	EP300	chr1:97559266-97560352	A549	lung:	n/a	n/a
4	FOSL2	chr1:97559522-97560349	A549	lung:	n/a	n/a
5	EP300	chr1:97559291-97560266	Hela-S3	cervix:	n/a	n/a
6	JUN	chr1:97559391-97560354	Hela-S3	cervix:	n/a	n/a
7	TEAD4	chr1:97559535-97560469	SK-N-SH	brain:	n/a	n/a
8	BRCA1	chr1:97559137-97560305	Hela-S3	cervix:	n/a	n/a
9	JUND	chr1:97559585-97560591	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr1:97559510-97560575	SK-N-SH	brain:	n/a	n/a
11	STAT3	chr1:97559355-97560240	MCF10A-Er-Src	breast:	n/a	chr1:97559944-97559955
12	FOS	chr1:97559302-97560437	MCF10A-Er-Src	breast:	n/a	chr1:97560061-97560072
13	FOS	chr1:97559857-97560258	MCF10A-Er-Src	breast:	n/a	chr1:97560061-97560072
14	CEBPB	chr1:97559273-97560284	A549	lung:	n/a	n/a
15	FOSL2	chr1:97559824-97560231	A549	lung:	n/a	n/a
16	GTF2F1	chr1:97559647-97560260	Hela-S3	cervix:	n/a	n/a
17	CEBPB	chr1:97559909-97560247	A549	lung:	n/a	n/a
18	POLR2A	chr1:97559237-97560384	PFSK-1	brain:	n/a	n/a
19	GATA3	chr1:97559064-97560639	SK-N-SH	brain:	n/a	chr1:97559577-97559587 chr1:97560021-97560029
20	MAX	chr1:97559713-97560260	A549	lung:	n/a	n/a
21	FOS	chr1:97559231-97560326	MCF10A-Er-Src	breast:	n/a	chr1:97560061-97560072
22	GATA2	chr1:97559465-97560783	HUVEC	blood vessel:	n/a	chr1:97559577-97559587 chr1:97560019-97560033
23	CEBPB	chr1:97559221-97560300	Hela-S3	cervix:	n/a	n/a
24	TCF12	chr1:97559174-97560540	SK-N-SH	brain:	n/a	n/a
25	TCF12	chr1:97559394-97560445	SK-N-SH	brain:	n/a	n/a
26	CHD2	chr1:97559493-97560286	Hela-S3	cervix:	n/a	n/a
27	JUND	chr1:97559264-97560454	SK-N-SH	brain:	n/a	n/a
28	TAF1	chr1:97559411-97560295	PFSK-1	brain:	n/a	n/a
29	YY1	chr1:97559703-97560337	SK-N-SH	brain:	n/a	n/a
30	RAD21	chr1:97559363-97560318	Hela-S3	cervix:	n/a	n/a
31	CEBPB	chr1:97559127-97560352	A549	lung:	n/a	n/a
32	GATA3	chr1:97559134-97560549	SK-N-SH	brain:	n/a	chr1:97559577-97559587 chr1:97560021-97560029
33	TBP	chr1:97559647-97560254	Hela-S3	cervix:	n/a	n/a
34	PBX3	chr1:97559245-97560375	SK-N-SH	brain:	n/a	n/a
35	MAX	chr1:97559654-97560333	A549	lung:	n/a	n/a
36	NFIC	chr1:97559747-97560356	SK-N-SH	brain:	n/a	n/a
37	JUND	chr1:97559371-97560306	Hela-S3	cervix:	n/a	n/a
38	STAT1	chr1:97559407-97560392	Hela-S3	cervix:	n/a	chr1:97559944-97559955
39	WRNIP1	chr1:97560066-97560248	GM12878	blood:	n/a	n/a
40	E2F4	chr1:97559925-97560226	MCF10A-Er-Src	breast:	n/a	n/a
41	SP1	chr1:97559214-97560344	A549	lung:	n/a	n/a
42	POLR2A	chr1:97560065-97560263	MCF10A-Er-Src	breast:	n/a	n/a
43	RCOR1	chr1:97559388-97560253	Hela-S3	cervix:	n/a	n/a
44	EP300	chr1:97559544-97560321	SK-N-SH	brain:	n/a	n/a
45	PBX3	chr1:97559228-97560394	SK-N-SH	brain:	n/a	n/a
46	FOSL2	chr1:97559729-97560454	SK-N-SH	brain:	n/a	n/a
47	JUND	chr1:97559481-97560493	SK-N-SH	brain:	n/a	n/a
48	EP300	chr1:97559230-97560454	SK-N-SH	brain:	n/a	n/a
49	FOSL2	chr1:97559537-97560526	SK-N-SH	brain:	n/a	n/a
50	USF2	chr1:97559875-97560399	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:96628387..96630261-chr1:97558478..97560909,2	MCF-7	breast:

Variant related genes	Relation type
DPYD-AS1	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12069444	1.00[AMR][1000 genomes]
rs290823	1.00[AMR][1000 genomes]
rs55737241	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55890675	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55896709	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56116315	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56283857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57607396	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58372929	1.00[AMR][1000 genomes]
rs59996661	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60455988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60480849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61208874	1.00[AMR][1000 genomes]
rs72726671	1.00[EUR][1000 genomes]
rs74104255	1.00[AMR][1000 genomes]
rs74104256	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74104257	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74104259	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74104311	1.00[AMR][1000 genomes]
rs74104313	1.00[AMR][1000 genomes]
rs74104319	1.00[AMR][1000 genomes]
rs74104321	1.00[AMR][1000 genomes]
rs74106608	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74106609	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74106636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74106640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74106641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74106643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74106677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74106679	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74106684	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74106701	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830692	chr1:97501492-97625153	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97538000-97603600	Weak transcription	Psoas Muscle	Psoas
2	chr1:97538600-97561800	Weak transcription	Right Ventricle	heart
3	chr1:97538600-97562200	Weak transcription	Left Ventricle	heart
4	chr1:97538600-97562200	Weak transcription	Lung	lung
5	chr1:97539600-97565000	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:97540000-97566800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:97540400-97575200	Weak transcription	Ovary	ovary
8	chr1:97542200-97562600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:97542400-97584800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:97542800-97562200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:97543000-97562600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr1:97545200-97561000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:97546200-97561400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:97549000-97562200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:97552600-97574600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:97556600-97560600	Enhancers	HUVEC	blood vessel
17	chr1:97557000-97564600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:97557200-97562000	Weak transcription	Primary T cells from cord blood	blood
19	chr1:97557600-97563000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:97557600-97565000	Weak transcription	Brain Substantia Nigra	brain
21	chr1:97557600-97565000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:97557600-97585000	Weak transcription	Brain Angular Gyrus	brain
23	chr1:97558000-97562200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:97558000-97562600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:97558000-97563000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:97558000-97572200	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:97558200-97562600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:97558200-97569400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr1:97558400-97564000	Weak transcription	Fetal Brain Male	brain
30	chr1:97558600-97562800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:97558600-97564600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:97558800-97560600	Enhancers	Hela-S3	cervix
33	chr1:97558800-97568400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:97559000-97560600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:97559000-97560600	Enhancers	HMEC	breast
36	chr1:97559000-97560600	Enhancers	NH-A	brain
37	chr1:97559000-97560600	Enhancers	NHEK	skin
38	chr1:97559000-97560600	Enhancers	Osteobl	bone
39	chr1:97559200-97560600	Strong transcription	Liver	Liver
40	chr1:97559400-97560400	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr1:97559400-97560400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:97559400-97560400	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr1:97559400-97560400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:97559400-97560400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:97559400-97560400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:97559400-97560400	Enhancers	NHDF-Ad	bronchial
47	chr1:97559600-97560400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:97559600-97560400	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr1:97559600-97560400	Strong transcription	Adipose Nuclei	Adipose
50	chr1:97559600-97560400	Enhancers	Placenta Amnion	Placenta Amnion

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