Variant report

Variant	rs3804546
Chromosome Location	chr6:4936634-4936635
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4932165..4934498-chr6:4934564..4936978,2	MCF-7	breast:
2	chr6:4934856..4938294-chr6:4940217..4942355,4	K562	blood:
3	chr6:4928518..4932053-chr6:4933158..4936712,4	K562	blood:
4	chr6:4936581..4938828-chr6:4939239..4942191,2	MCF-7	breast:
5	chr6:4807577..4808212-chr6:4936011..4936824,2	MCF-7	breast:
6	chr6:4804988..4807202-chr6:4935507..4937901,2	MCF-7	breast:
7	chr6:4920596..4921579-chr6:4936621..4937155,2	MCF-7	breast:
8	chr6:4895552..4898215-chr6:4935545..4937308,2	K562	blood:

Variant related genes	Relation type
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12199520	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12213161	0.85[EUR][1000 genomes]
rs13208366	0.95[ASN][1000 genomes]
rs2039904	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789792	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3789793	0.83[EUR][1000 genomes]
rs3789796	0.86[EUR][1000 genomes]
rs3789797	0.86[EUR][1000 genomes]
rs3789799	0.83[EUR][1000 genomes]
rs3804547	0.97[ASN][1000 genomes]
rs6913671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6914821	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7738117	0.87[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7757702	0.83[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4913200-4941000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:4913600-4938000	Weak transcription	Primary B cells from peripheral blood	blood
3	chr6:4915800-4942400	Weak transcription	Aorta	Aorta
4	chr6:4923000-4937800	Weak transcription	Primary T cells from cord blood	blood
5	chr6:4925600-4941600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:4927600-4940200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:4929400-4941600	Weak transcription	Osteobl	bone
8	chr6:4930200-4939800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr6:4930800-4940200	Weak transcription	NH-A	brain
10	chr6:4930800-4940600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr6:4932000-4942000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:4932200-4940800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:4932200-4945000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:4932400-4936800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:4932400-4936800	Weak transcription	NHLF	lung
16	chr6:4932400-4941000	Weak transcription	HSMM	muscle
17	chr6:4932400-4941400	Weak transcription	NHDF-Ad	bronchial
18	chr6:4932400-4941600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:4932400-4942000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:4932400-4942400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:4932600-4940600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:4932600-4941000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:4932600-4942200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:4932600-4944200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr6:4932600-4944600	Weak transcription	Colonic Mucosa	Colon
26	chr6:4932800-4944400	Weak transcription	Thymus	Thymus
27	chr6:4933000-4938000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:4933000-4940200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:4933000-4942200	Weak transcription	Fetal Intestine Large	intestine
30	chr6:4933000-4944400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:4933200-4938200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:4933200-4940600	Weak transcription	HMEC	breast
33	chr6:4933200-4941600	Weak transcription	Ovary	ovary
34	chr6:4933400-4941000	Weak transcription	Psoas Muscle	Psoas
35	chr6:4933400-4941800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:4933400-4942000	Weak transcription	Colon Smooth Muscle	Colon
37	chr6:4933400-4944600	Weak transcription	Pancreas	Pancrea
38	chr6:4933600-4936800	Weak transcription	HUVEC	blood vessel
39	chr6:4933600-4937400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:4933600-4938400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:4933600-4940800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr6:4933600-4941000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:4933600-4942400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:4933600-4950000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:4933800-4936800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr6:4933800-4940800	Weak transcription	Hela-S3	cervix
47	chr6:4933800-4941000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr6:4933800-4941400	Weak transcription	Right Ventricle	heart
49	chr6:4933800-4944400	Weak transcription	Gastric	stomach
50	chr6:4934200-4941400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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