Variant report

Variant	rs57744001
Chromosome Location	chr6:35569896-35569897
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35556174..35558038-chr6:35568074..35570018,2	MCF-7	breast:
2	chr6:35569080..35571886-chr6:35578930..35581729,3	K562	blood:
3	chr6:35560229..35562371-chr6:35569812..35572139,2	K562	blood:
4	chr6:35568378..35571092-chr6:35588420..35590433,2	K562	blood:
5	chr6:35569328..35571242-chr6:35694203..35697071,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000096060	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs4711421	1.00[EUR][1000 genomes]
rs57155120	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57985230	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58549426	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59520042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59590692	1.00[EUR][1000 genomes]
rs60103601	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60867971	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61731466	1.00[EUR][1000 genomes]
rs9470086	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS 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 miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv2761067	chr6:35471246-35573245	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1031987	chr6:35476562-35579375	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv462913	chr6:35502202-35592744	Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv602923	chr6:35502202-35592744	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv517211	chr6:35502202-35607571	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1023091	chr6:35502604-35573233	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv1017625	chr6:35505311-35576552	Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv1019593	chr6:35505311-35579375	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv602924	chr6:35505311-35750299	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
12	nsv1022049	chr6:35506731-35576552	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	nsv1025296	chr6:35507179-35579375	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
14	nsv885801	chr6:35537406-35671651	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
15	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35541200-35570200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:35545000-35601800	Weak transcription	Fetal Intestine Small	intestine
3	chr6:35558600-35580400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr6:35565400-35570400	Weak transcription	Colonic Mucosa	Colon
5	chr6:35565400-35571600	Weak transcription	Spleen	Spleen
6	chr6:35565400-35579800	Weak transcription	Ovary	ovary
7	chr6:35566200-35571800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:35567800-35570000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr6:35567800-35570200	Enhancers	Fetal Lung	lung
10	chr6:35567800-35570600	Bivalent Enhancer	Dnd41	blood
11	chr6:35567800-35570800	Enhancers	Fetal Stomach	stomach
12	chr6:35567800-35571200	Enhancers	Stomach Mucosa	stomach
13	chr6:35568000-35570600	Enhancers	Fetal Kidney	kidney
14	chr6:35568000-35570800	Enhancers	Primary B cells from peripheral blood	blood
15	chr6:35568000-35571000	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr6:35568200-35570000	Enhancers	Liver	Liver
17	chr6:35568200-35572000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:35568400-35570000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:35568400-35570400	Flanking Active TSS	HUVEC	blood vessel
20	chr6:35568400-35570800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:35568400-35570800	Flanking Active TSS	NHEK	skin
22	chr6:35568400-35571000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr6:35568400-35571000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr6:35568400-35571000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr6:35568400-35571200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr6:35568600-35570200	Active TSS	Right Atrium	heart
27	chr6:35568600-35570800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr6:35568600-35570800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr6:35568600-35570800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr6:35568600-35571000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr6:35568600-35571000	Enhancers	Fetal Brain Female	brain
32	chr6:35568600-35571200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:35568800-35570200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:35568800-35570600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:35568800-35570600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:35568800-35570600	Enhancers	Brain Germinal Matrix	brain
37	chr6:35568800-35570800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:35568800-35570800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:35568800-35570800	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr6:35568800-35570800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:35568800-35570800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:35568800-35571200	Enhancers	Hela-S3	cervix
43	chr6:35568800-35572000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr6:35569000-35570000	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr6:35569000-35570000	Flanking Active TSS	NH-A	brain
46	chr6:35569000-35570200	Flanking Active TSS	HepG2	liver
47	chr6:35569000-35570600	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr6:35569000-35570600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr6:35569000-35570600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:35569000-35570600	Flanking Active TSS	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links