Variant report

Variant	rs6660069
Chromosome Location	chr1:9949013-9949014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9943092..9944690-chr1:9948920..9950860,2	MCF-7	breast:
2	chr1:9948830..9950649-chr1:9965085..9967755,2	K562	blood:
3	chr1:9944846..9946989-chr1:9947780..9950695,2	MCF-7	breast:
4	chr1:9944042..9945752-chr1:9947659..9949631,2	K562	blood:
5	chr1:9948461..9950463-chr1:9972142..9973829,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17034420	0.87[AMR][1000 genomes]
rs4417070	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6541068	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6681118	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs6686710	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6695334	0.84[AMR][1000 genomes]
rs72858042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72858053	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74054138	0.81[AMR][1000 genomes]
rs7529783	0.81[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:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9930800-9949600	Weak transcription	Fetal Lung	lung
2	chr1:9932600-9960200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr1:9935600-9949200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr1:9935600-9949400	Weak transcription	HUVEC	blood vessel
5	chr1:9935600-9950200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:9935600-9960800	Weak transcription	Fetal Intestine Large	intestine
7	chr1:9935800-9950800	Weak transcription	Aorta	Aorta
8	chr1:9936000-9950000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:9936000-9950000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:9936200-9949800	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:9936400-9960200	Weak transcription	Liver	Liver
12	chr1:9937200-9950000	Weak transcription	Fetal Brain Male	brain
13	chr1:9938400-9950000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:9938600-9952800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:9938800-9949600	Weak transcription	Stomach Mucosa	stomach
16	chr1:9940800-9952400	Strong transcription	Fetal Intestine Small	intestine
17	chr1:9942400-9950000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:9942400-9950600	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:9942600-9949800	Weak transcription	Osteobl	bone
20	chr1:9942600-9950000	Weak transcription	HepG2	liver
21	chr1:9942800-9949200	Weak transcription	NHLF	lung
22	chr1:9943000-9949800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:9943000-9960200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:9943200-9961600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:9943600-9960800	Weak transcription	Primary T cells from cord blood	blood
26	chr1:9944200-9949200	Weak transcription	Spleen	Spleen
27	chr1:9944600-9950600	Weak transcription	Ovary	ovary
28	chr1:9945000-9949200	Strong transcription	Fetal Stomach	stomach
29	chr1:9945200-9950000	Weak transcription	Brain Anterior Caudate	brain
30	chr1:9945200-9950000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:9945200-9950000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:9945400-9950000	Weak transcription	Fetal Brain Female	brain
33	chr1:9946600-9950600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:9946800-9949400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:9946800-9950000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:9946800-9950000	Weak transcription	Brain Angular Gyrus	brain
37	chr1:9946800-9950000	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:9946800-9950000	Weak transcription	Brain Substantia Nigra	brain
39	chr1:9946800-9950000	Weak transcription	HSMMtube	muscle
40	chr1:9946800-9950200	Weak transcription	A549	lung
41	chr1:9946800-9950200	Weak transcription	K562	blood
42	chr1:9947000-9950600	Weak transcription	Colonic Mucosa	Colon
43	chr1:9947000-9952000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr1:9947000-9953600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr1:9947200-9949800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:9947200-9950000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:9947200-9950000	Weak transcription	Fetal Heart	heart
48	chr1:9947200-9950600	Weak transcription	Gastric	stomach
49	chr1:9947400-9949200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:9947400-9949200	Weak transcription	HSMM	muscle

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