Variant report

Variant	rs6840561
Chromosome Location	chr4:110385601-110385602
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:110381168..110383587-chr4:110385101..110388629,3	K562	blood:
2	chr4:110384184..110389120-chr4:110389509..110396492,10	K562	blood:
3	chr4:110384184..110386804-chr4:110389509..110391304,2	K562	blood:
4	chr4:110378967..110381063-chr4:110384891..110387405,2	K562	blood:
5	chr4:110365032..110367988-chr4:110384453..110386346,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10003981	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10005225	1.00[EUR][1000 genomes]
rs10008457	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10009463	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10011971	1.00[EUR][1000 genomes]
rs10016533	0.84[AFR][1000 genomes]
rs10020652	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10030694	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17040433	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17040466	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17040498	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28412073	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28460762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28541279	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28595287	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28597954	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28663368	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28680423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28723468	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28829974	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57705376	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6533431	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6533432	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6812917	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6834714	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6837083	1.00[EUR][1000 genomes]
rs6838597	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6852062	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6854516	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72898791	1.00[EUR][1000 genomes]
rs7665738	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7667502	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7674196	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7677736	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7681265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7685647	1.00[EUR][1000 genomes]
rs7697001	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997563	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][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	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110363600-110398400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:110366000-110391400	Weak transcription	Small Intestine	intestine
3	chr4:110371400-110393200	Weak transcription	Stomach Mucosa	stomach
4	chr4:110371600-110393400	Weak transcription	HSMMtube	muscle
5	chr4:110377600-110386200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:110378800-110415800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr4:110382800-110390400	Strong transcription	NH-A	brain
8	chr4:110383000-110385800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:110383000-110385800	Strong transcription	Fetal Intestine Small	intestine
10	chr4:110383000-110386800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:110383000-110387800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:110383000-110387800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:110383200-110385800	Strong transcription	Fetal Stomach	stomach
14	chr4:110383200-110386200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:110383200-110386200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:110383200-110386400	Strong transcription	Thymus	Thymus
17	chr4:110383200-110386600	Strong transcription	Fetal Muscle Leg	muscle
18	chr4:110383200-110386800	Strong transcription	Primary T cells from cord blood	blood
19	chr4:110383200-110387000	Strong transcription	Fetal Intestine Large	intestine
20	chr4:110383400-110387000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:110383400-110387000	Strong transcription	Fetal Muscle Trunk	muscle
22	chr4:110383400-110388000	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr4:110383400-110396000	Strong transcription	Fetal Thymus	thymus
24	chr4:110383400-110397600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr4:110383600-110385800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:110383600-110386000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:110383600-110386400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:110383600-110386800	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr4:110383600-110386800	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr4:110383600-110386800	Strong transcription	HepG2	liver
31	chr4:110383600-110386800	Strong transcription	K562	blood
32	chr4:110383600-110387000	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr4:110383600-110387000	Strong transcription	Dnd41	blood
34	chr4:110383600-110387400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr4:110383600-110388200	Strong transcription	HUVEC	blood vessel
36	chr4:110383600-110391600	Weak transcription	Psoas Muscle	Psoas
37	chr4:110383600-110392000	Strong transcription	HSMM	muscle
38	chr4:110383800-110385800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:110383800-110386400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr4:110383800-110387000	Strong transcription	Primary B cells from peripheral blood	blood
41	chr4:110383800-110387400	Strong transcription	Liver	Liver
42	chr4:110383800-110387400	Strong transcription	NHLF	lung
43	chr4:110383800-110387800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr4:110383800-110389400	Strong transcription	Primary hematopoietic stem cells	blood
45	chr4:110384000-110385800	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr4:110384000-110385800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:110384000-110385800	Strong transcription	Brain Cingulate Gyrus	brain
48	chr4:110384000-110385800	Strong transcription	Fetal Heart	heart
49	chr4:110384000-110386000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr4:110384000-110386000	Strong transcription	Placenta Amnion	Placenta Amnion

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