Variant report

Variant	rs6667509
Chromosome Location	chr1:215796350-215796351
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:215795506..215798037-chr1:215804962..215807683,2	MCF-7	breast:
2	chr1:215794954..215796853-chr1:215797386..215800956,3	K562	blood:
3	chr1:215795233..215796830-chr1:215807940..215809672,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12077184	0.82[EUR][1000 genomes]
rs12080379	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs12080437	0.90[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1557172	0.86[JPT][hapmap]
rs1819740	0.86[JPT][hapmap]
rs2677113	0.86[JPT][hapmap]
rs2797392	0.86[JPT][hapmap]
rs3753837	0.86[JPT][hapmap]
rs3753838	0.86[JPT][hapmap]
rs3767253	1.00[JPT][hapmap]
rs3767260	0.86[JPT][hapmap]
rs3767262	0.86[JPT][hapmap]
rs6540901	1.00[JPT][hapmap]
rs6689680	0.86[JPT][hapmap]
rs7531580	1.00[JPT][hapmap]
rs7545425	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796390	chr1:215561548-215799074	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv430324	chr1:215649163-216082605	Strong transcription Enhancers Weak transcription Active TSS 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	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6667509	SLC30A1	cis	parietal	SCAN
rs6667509	C1orf97	cis	cerebellum	SCAN
rs6667509	VASH2	cis	parietal	SCAN
rs6667509	SMYD2	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215741800-215809800	Weak transcription	Colonic Mucosa	Colon
2	chr1:215750000-215805000	Weak transcription	Lung	lung
3	chr1:215750200-215804400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:215750200-215809200	Weak transcription	Gastric	stomach
5	chr1:215755800-215804800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:215773800-215798600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:215779400-215799200	Weak transcription	Psoas Muscle	Psoas
8	chr1:215781000-215797200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:215781200-215797400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:215782200-215799400	Weak transcription	Fetal Heart	heart
11	chr1:215782800-215797200	Weak transcription	Dnd41	blood
12	chr1:215783000-215798800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:215784800-215796600	Weak transcription	Spleen	Spleen
14	chr1:215786600-215809400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:215786800-215797400	Weak transcription	Fetal Brain Female	brain
16	chr1:215786800-215798200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:215786800-215799000	Weak transcription	Small Intestine	intestine
18	chr1:215786800-215801000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:215787200-215796400	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:215787200-215798400	Weak transcription	Primary T cells from cord blood	blood
21	chr1:215787200-215800600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:215787200-215810200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:215787400-215797000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:215787600-215801800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:215789000-215797000	Strong transcription	Fetal Intestine Large	intestine
26	chr1:215789000-215797000	Strong transcription	Fetal Muscle Trunk	muscle
27	chr1:215789000-215799200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:215789200-215797000	Strong transcription	Adipose Nuclei	Adipose
29	chr1:215789200-215797400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:215790200-215797600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:215790400-215797000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:215791000-215804400	Weak transcription	Esophagus	oesophagus
33	chr1:215791000-215805000	Weak transcription	Fetal Intestine Small	intestine
34	chr1:215791200-215796400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:215791400-215796400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:215791400-215796800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:215791400-215797000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr1:215791600-215797400	Strong transcription	Fetal Kidney	kidney
39	chr1:215791600-215798000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:215791600-215799400	Weak transcription	Right Ventricle	heart
41	chr1:215791800-215797600	Strong transcription	Osteobl	bone
42	chr1:215792000-215797000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr1:215792200-215800000	Strong transcription	Liver	Liver
44	chr1:215792400-215810200	Weak transcription	Aorta	Aorta
45	chr1:215792600-215796600	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:215792600-215798800	Weak transcription	Brain Substantia Nigra	brain
47	chr1:215792600-215801800	Weak transcription	Fetal Stomach	stomach
48	chr1:215792600-215802800	Weak transcription	Fetal Brain Male	brain
49	chr1:215792600-215804400	Weak transcription	NHEK	skin
50	chr1:215792600-215809800	Weak transcription	Pancreas	Pancrea

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