Variant report

Variant	rs10461349
Chromosome Location	chr4:57848282-57848283
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	PBX3	chr4:57847768-57848507	SK-N-SH	brain:	n/a	n/a
2	ATF3	chr4:57847999-57848361	K562	blood:	n/a	n/a
3	POLR2A	chr4:57848080-57848417	HUVEC	blood vessel:	n/a	n/a
4	TEAD4	chr4:57847891-57848479	K562	blood:	n/a	n/a
5	JUND	chr4:57848085-57848298	HepG2	liver:	n/a	n/a
6	TCF12	chr4:57847849-57848601	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr4:57848096-57848404	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr4:57847836-57848572	SK-N-SH	brain:	n/a	n/a
9	JUN	chr4:57848042-57848294	HepG2	liver:	n/a	chr4:57848214-57848227
10	FOS	chr4:57847968-57848395	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr4:57847880-57848619	HUVEC	blood vessel:	n/a	n/a
12	TEAD4	chr4:57847887-57848402	K562	blood:	n/a	n/a
13	GATA1	chr4:57847971-57848591	PBDE	blood:	n/a	n/a
14	RCOR1	chr4:57847876-57848404	K562	blood:	n/a	n/a
15	RCOR1	chr4:57848037-57848396	K562	blood:	n/a	n/a
16	ARID3A	chr4:57847839-57848322	K562	blood:	n/a	n/a
17	CEBPB	chr4:57848080-57848321	IMR90	lung:	n/a	n/a
18	CUX1	chr4:57847899-57848351	K562	blood:	n/a	n/a
19	JUND	chr4:57847939-57848499	SK-N-SH	brain:	n/a	n/a
20	GATA3	chr4:57847784-57848481	SK-N-SH	brain:	n/a	n/a
21	GATA2	chr4:57847961-57848502	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr4:57848210-57848307	IMR90	lung:	n/a	n/a
23	PRDM1	chr4:57847987-57848333	Hela-S3	cervix:	n/a	chr4:57848152-57848167
24	BHLHE40	chr4:57848172-57848392	K562	blood:	n/a	n/a
25	JUN	chr4:57847723-57848414	HUVEC	blood vessel:	n/a	chr4:57848214-57848227
26	POLR2A	chr4:57847881-57848541	HUVEC	blood vessel:	n/a	n/a
27	ATF1	chr4:57847995-57848373	K562	blood:	n/a	n/a
28	EP300	chr4:57847892-57848450	K562	blood:	n/a	n/a
29	TBL1XR1	chr4:57847889-57848364	K562	blood:	n/a	n/a
30	JUN	chr4:57847766-57848536	K562	blood:	n/a	chr4:57848214-57848227
31	JUN	chr4:57847979-57848513	K562	blood:	n/a	chr4:57848214-57848227
32	POLR2A	chr4:57847485-57848489	K562	blood:	n/a	n/a
33	JUN	chr4:57848016-57848424	K562	blood:	n/a	chr4:57848214-57848227
34	JUN	chr4:57847967-57848407	K562	blood:	n/a	chr4:57848214-57848227
35	JUND	chr4:57847845-57848460	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57771524..57779492-chr4:57841270..57849741,26	K562	blood:
2	chr4:57848130..57850979-chr4:57885683..57887962,2	K562	blood:
3	chr4:57847527..57849310-chr4:57850020..57851620,2	MCF-7	breast:

Variant related genes	Relation type
NOA1	TF binding region
ENSG00000084093	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10020462	0.94[JPT][hapmap]
rs10023088	0.94[JPT][hapmap]
rs1056364	0.94[JPT][hapmap]
rs11573125	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11573126	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12498216	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12506598	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12512295	0.81[ASN][1000 genomes]
rs12621	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12650737	0.94[JPT][hapmap]
rs1277308	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1403233	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1626594	0.85[ASN][1000 genomes]
rs17087265	0.82[JPT][hapmap]
rs1713982	0.84[ASN][1000 genomes]
rs1713983	0.84[ASN][1000 genomes]
rs1718830	0.84[ASN][1000 genomes]
rs1718831	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1718837	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1718863	0.84[ASN][1000 genomes]
rs1718864	0.84[ASN][1000 genomes]
rs1718878	0.85[ASN][1000 genomes]
rs2276897	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412774	0.82[ASN][1000 genomes]
rs3775082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796532	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3821994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4864609	0.85[ASN][1000 genomes]
rs56763474	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60292561	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61337636	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67479587	0.85[ASN][1000 genomes]
rs6843644	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs73167819	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73167841	1.00[EUR][1000 genomes];0.90[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	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer 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 target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57846000-57848400	Weak transcription	Gastric	stomach
2	chr4:57846000-57849400	Enhancers	Brain Angular Gyrus	brain
3	chr4:57846000-57852000	Weak transcription	Aorta	Aorta
4	chr4:57846000-57853600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:57846000-57855600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:57846000-57881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:57846200-57848400	Enhancers	Liver	Liver
8	chr4:57846200-57848400	Enhancers	Fetal Brain Male	brain
9	chr4:57846200-57848400	Enhancers	Fetal Lung	lung
10	chr4:57846200-57849000	Flanking Active TSS	HUVEC	blood vessel
11	chr4:57846200-57849400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr4:57846200-57850800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr4:57846200-57851400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:57846200-57851800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr4:57846200-57851800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr4:57846200-57851800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:57846200-57853000	Weak transcription	Fetal Kidney	kidney
18	chr4:57846200-57853600	Weak transcription	Esophagus	oesophagus
19	chr4:57846200-57861600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr4:57846200-57861800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:57846400-57848400	Enhancers	Brain Hippocampus Middle	brain
22	chr4:57846400-57848400	Enhancers	Fetal Heart	heart
23	chr4:57846400-57848400	Enhancers	Fetal Intestine Large	intestine
24	chr4:57846400-57848600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:57846400-57849000	Weak transcription	Psoas Muscle	Psoas
26	chr4:57846400-57849400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr4:57846400-57849800	Enhancers	Primary T cells fromperipheralblood	blood
28	chr4:57846600-57848600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr4:57846600-57848800	Genic enhancers	Fetal Intestine Small	intestine
30	chr4:57846600-57849000	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr4:57846600-57849400	Enhancers	Small Intestine	intestine
32	chr4:57846600-57850000	Genic enhancers	Primary T cells from cord blood	blood
33	chr4:57846600-57851800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:57846600-57852200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr4:57846600-57853200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr4:57846600-57861200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr4:57846800-57848600	Enhancers	Thymus	Thymus
38	chr4:57846800-57849200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:57846800-57849600	Enhancers	HepG2	liver
40	chr4:57846800-57851200	Weak transcription	Lung	lung
41	chr4:57846800-57852000	Weak transcription	NHDF-Ad	bronchial
42	chr4:57846800-57852200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:57846800-57852600	Weak transcription	HSMMtube	muscle
44	chr4:57846800-57900000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:57847000-57848400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:57847000-57848400	Enhancers	Duodenum Mucosa	Duodenum
47	chr4:57847000-57848400	Enhancers	HMEC	breast
48	chr4:57847000-57848600	Genic enhancers	Primary B cells from cord blood	blood
49	chr4:57847000-57850000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:57847000-57850200	Enhancers	Primary T helper cells fromperipheralblood	blood

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