Variant report

Variant	rs600674
Chromosome Location	chr1:84701251-84701252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:84699628..84701684-chr1:84763119..84765204,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203943	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1027694	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11163929	0.90[EUR][1000 genomes]
rs11163932	0.87[ASN][1000 genomes]
rs12041490	0.90[EUR][1000 genomes]
rs12406360	0.90[EUR][1000 genomes]
rs1402696	0.92[ASN][1000 genomes]
rs1494312	0.91[ASN][1000 genomes]
rs1521520	0.82[ASN][1000 genomes]
rs17365096	0.84[EUR][1000 genomes]
rs2389717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4906988	0.84[ASN][1000 genomes]
rs4907047	0.90[ASN][1000 genomes]
rs4907049	0.84[ASN][1000 genomes]
rs4907051	0.83[ASN][1000 genomes]
rs583720	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs600902	0.98[ASN][1000 genomes]
rs611467	0.90[EUR][1000 genomes]
rs612848	0.98[ASN][1000 genomes]
rs615468	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs615726	0.94[ASN][1000 genomes]
rs632802	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs655977	0.92[ASN][1000 genomes]
rs6576697	0.85[ASN][1000 genomes]
rs6703471	0.83[ASN][1000 genomes]
rs674494	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871643	chr1:84628655-84705481	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv871538	chr1:84633116-84717983	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv830414	chr1:84636738-84824651	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv1816427	chr1:84670816-84715634	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	esv1823244	chr1:84670816-84715634	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	esv1824568	chr1:84670816-84715634	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	esv1822734	chr1:84678418-84715634	ZNF genes & repeats Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	esv1845114	chr1:84678418-84715634	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
9	esv1851921	chr1:84678418-84715634	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs600674	CLCA1	cis	cerebellum	SCAN
rs600674	TTLL7	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84657600-84708000	Weak transcription	Left Ventricle	heart
2	chr1:84659800-84701400	Weak transcription	NHLF	lung
3	chr1:84666800-84710200	Weak transcription	HSMMtube	muscle
4	chr1:84672600-84711200	Weak transcription	Brain Substantia Nigra	brain
5	chr1:84675200-84712800	Weak transcription	NH-A	brain
6	chr1:84675800-84705000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:84685400-84705400	Weak transcription	HUVEC	blood vessel
8	chr1:84685400-84705600	Weak transcription	Brain Germinal Matrix	brain
9	chr1:84685600-84713400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:84690000-84719400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:84690200-84707400	Weak transcription	Right Ventricle	heart
12	chr1:84690400-84702600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:84690400-84705000	Weak transcription	Aorta	Aorta
14	chr1:84690400-84711800	Weak transcription	Spleen	Spleen
15	chr1:84691200-84712200	Weak transcription	Pancreas	Pancrea
16	chr1:84691400-84705000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:84691400-84707000	Weak transcription	Fetal Stomach	stomach
18	chr1:84691600-84705000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:84697400-84705000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:84698600-84705400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:84699000-84707000	Weak transcription	Psoas Muscle	Psoas
22	chr1:84699600-84713000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:84699800-84711600	Weak transcription	A549	lung
24	chr1:84700200-84702800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:84700400-84701400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:84700400-84701400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:84700400-84701400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
28	chr1:84700400-84702200	Strong transcription	Thymus	Thymus
29	chr1:84700400-84706200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:84700600-84701400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:84700600-84701400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
32	chr1:84700600-84701400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:84700600-84701400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr1:84700600-84701400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
35	chr1:84700600-84701400	Strong transcription	Fetal Brain Female	brain
36	chr1:84700600-84701400	Strong transcription	HSMM	muscle
37	chr1:84700600-84701800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr1:84700600-84701800	Strong transcription	Brain Anterior Caudate	brain
39	chr1:84700600-84701800	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr1:84700600-84701800	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr1:84700600-84702000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:84700600-84702000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:84700600-84702600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:84700600-84702800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:84700600-84703400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:84700600-84705800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr1:84700600-84705800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:84700600-84705800	Strong transcription	Brain Hippocampus Middle	brain
49	chr1:84700600-84706000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr1:84700600-84706200	Strong transcription	Fetal Thymus	thymus

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