Variant report

Variant	rs7549028
Chromosome Location	chr1:78447728-78447729
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78447431..78449969-chr1:78468449..78471656,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DNAJB4-1	chr1:78444779-78456066	NONHSAT004062

Variant related genes	Relation type
ENSG00000273338	Chromatin interaction
ENSG00000162616	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs41312643	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6604877	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs6666107	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs6679645	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs6686829	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6694656	1.00[YRI][hapmap]
rs74092331	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7523258	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs7548467	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9659817	1.00[CEU][hapmap]
rs9661421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv518855	chr1:78416669-78456355	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78445800-78449600	Weak transcription	Stomach Mucosa	stomach
2	chr1:78445800-78449800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:78446000-78448200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:78446000-78448200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:78446000-78449800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:78446000-78449800	Weak transcription	Small Intestine	intestine
7	chr1:78446000-78451800	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr1:78446000-78452600	Weak transcription	Gastric	stomach
9	chr1:78446000-78455600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:78446000-78458600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:78446000-78458800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:78446000-78461000	Weak transcription	Placenta	Placenta
13	chr1:78446200-78447800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr1:78446200-78448400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:78446200-78449400	Weak transcription	Fetal Intestine Large	intestine
16	chr1:78446200-78451800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:78446200-78452400	Weak transcription	Psoas Muscle	Psoas
18	chr1:78446200-78452600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:78446200-78457200	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:78446200-78461200	Weak transcription	Fetal Stomach	stomach
21	chr1:78446200-78469600	Weak transcription	Thymus	Thymus
22	chr1:78446400-78447800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:78446400-78448000	Enhancers	Brain Hippocampus Middle	brain
24	chr1:78446400-78451800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:78446400-78458200	Weak transcription	Fetal Thymus	thymus
26	chr1:78446400-78469800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr1:78446400-78470200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr1:78446600-78447800	Enhancers	Brain Anterior Caudate	brain
29	chr1:78446600-78448000	Enhancers	Dnd41	blood
30	chr1:78446600-78448200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:78446600-78449400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:78446600-78449600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:78446600-78449600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:78446600-78449600	Weak transcription	Fetal Intestine Small	intestine
35	chr1:78446600-78449600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:78446600-78449800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:78446600-78450000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:78446600-78450000	Weak transcription	Fetal Heart	heart
39	chr1:78446600-78450600	Weak transcription	HSMMtube	muscle
40	chr1:78446600-78450800	Weak transcription	Primary B cells from cord blood	blood
41	chr1:78446600-78450800	Enhancers	HepG2	liver
42	chr1:78446600-78451800	Weak transcription	Right Atrium	heart
43	chr1:78446600-78457200	Weak transcription	Primary T cells from cord blood	blood
44	chr1:78446600-78459200	Weak transcription	Fetal Brain Female	brain
45	chr1:78446600-78460800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:78446600-78461200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr1:78446600-78468000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:78446600-78468400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:78446600-78468800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:78446600-78468800	Weak transcription	Adipose Nuclei	Adipose

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