Variant report

Variant	rs6541067
Chromosome Location	chr1:9929974-9929975
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	chr1:9929452..9932865-chr1:10092666..10095157,3	K562	blood:

Variant related genes	Relation type
ENSG00000130939	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11808614	0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57237552	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61785591	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61785593	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61785598	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6659441	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6680882	0.81[YRI][hapmap]
rs6686017	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6690524	0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74054125	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74054138	0.83[AMR][1000 genomes]
rs7529783	0.82[YRI][hapmap];0.83[AMR][1000 genomes]
rs7536748	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7537879	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7554923	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv871146	chr1:9897001-9951288	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS 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
6	nsv545380	chr1:9918183-9987007	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9904400-9930000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:9904600-9935000	Weak transcription	Osteobl	bone
3	chr1:9904800-9946000	Weak transcription	Fetal Kidney	kidney
4	chr1:9907000-9930000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:9910000-9935000	Weak transcription	NHLF	lung
6	chr1:9911000-9930400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:9911200-9932400	Weak transcription	Fetal Heart	heart
8	chr1:9915800-9935200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:9917800-9934400	Strong transcription	Fetal Intestine Small	intestine
10	chr1:9918000-9932800	Strong transcription	Fetal Brain Female	brain
11	chr1:9918200-9932800	Strong transcription	Lung	lung
12	chr1:9918600-9943800	Weak transcription	Small Intestine	intestine
13	chr1:9920000-9930400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:9920200-9930400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr1:9920200-9932200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:9920200-9935200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:9920400-9930000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:9920400-9930400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:9921000-9934800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:9921200-9932600	Weak transcription	HSMMtube	muscle
21	chr1:9921400-9932400	Weak transcription	HSMM	muscle
22	chr1:9921600-9930000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:9921800-9934800	Weak transcription	Right Atrium	heart
24	chr1:9922000-9933200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:9923800-9935200	Weak transcription	A549	lung
26	chr1:9924200-9934400	Strong transcription	Fetal Stomach	stomach
27	chr1:9924200-9935200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:9924200-9935200	Weak transcription	Brain Substantia Nigra	brain
29	chr1:9925800-9930600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:9925800-9931800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:9925800-9932000	Strong transcription	Fetal Intestine Large	intestine
32	chr1:9925800-9932400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:9925800-9933400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:9925800-9933600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr1:9926000-9932600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:9926000-9932800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:9926200-9930400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:9926200-9932600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:9926200-9932600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:9926200-9933200	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr1:9926400-9930000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:9926800-9931800	Strong transcription	Pancreas	Pancrea
43	chr1:9927000-9932200	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr1:9927400-9933200	Strong transcription	Adipose Nuclei	Adipose
45	chr1:9927600-9930400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:9927600-9941800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:9927800-9930400	Strong transcription	Brain Hippocampus Middle	brain
48	chr1:9927800-9932000	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:9927800-9932600	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:9927800-9933000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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