Variant report

Variant	rs6683757
Chromosome Location	chr1:227959417-227959418
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	chr1:227953908..227955707-chr1:227958879..227960406,2	K562	blood:
2	chr1:227955528..227959696-chr1:228132593..228135770,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143816	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10799447	0.90[JPT][hapmap]
rs10799448	0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10799449	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10916205	0.88[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10916207	0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12138074	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17555357	0.90[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2236359	0.90[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2281708	0.88[ASN][1000 genomes]
rs2295994	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6672002	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6683869	0.90[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6696944	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6697054	0.89[ASN][1000 genomes]
rs7526021	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv468238	chr1:227935762-228045748	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv549272	chr1:227935762-228045748	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
12	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6683757	C1orf142	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227946000-227960400	Strong transcription	Fetal Brain Female	brain
2	chr1:227950800-227963000	Strong transcription	Brain Germinal Matrix	brain
3	chr1:227950800-227974200	Weak transcription	Small Intestine	intestine
4	chr1:227951000-227963200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:227951200-227974400	Weak transcription	Right Atrium	heart
6	chr1:227951400-227963200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:227951600-227961800	Strong transcription	Fetal Stomach	stomach
8	chr1:227951600-227963600	Weak transcription	HUVEC	blood vessel
9	chr1:227951800-227970600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:227952000-227962000	Weak transcription	NHDF-Ad	bronchial
11	chr1:227952200-227960200	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:227952200-227962400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:227953200-227959800	Strong transcription	NHLF	lung
14	chr1:227953200-227960400	Strong transcription	Stomach Smooth Muscle	stomach
15	chr1:227954000-227959800	Strong transcription	Dnd41	blood
16	chr1:227954000-227962600	Strong transcription	Adipose Nuclei	Adipose
17	chr1:227954400-227963800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:227954400-227974600	Weak transcription	HMEC	breast
19	chr1:227954600-227960200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:227954600-227960200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:227954600-227963200	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:227954600-227963200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:227954800-227964400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr1:227955000-227962200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr1:227955200-227959800	Strong transcription	Ovary	ovary
26	chr1:227955200-227964800	Strong transcription	Liver	Liver
27	chr1:227955400-227959600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:227955400-227960000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr1:227955400-227960200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:227955400-227961000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:227955600-227960200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:227955600-227960200	Strong transcription	Gastric	stomach
33	chr1:227955600-227960200	Strong transcription	Pancreas	Pancrea
34	chr1:227955600-227960200	Strong transcription	Spleen	Spleen
35	chr1:227955600-227960400	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:227955600-227960600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:227955600-227960600	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr1:227955600-227961200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr1:227955600-227961800	Weak transcription	Fetal Heart	heart
40	chr1:227955600-227962200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:227955600-227965000	Strong transcription	Placenta	Placenta
42	chr1:227955600-227973200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:227955600-227974000	Weak transcription	Fetal Brain Male	brain
44	chr1:227955800-227972400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr1:227955800-227974800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:227955800-227975200	Weak transcription	Hela-S3	cervix
47	chr1:227956000-227961200	Weak transcription	HSMM	muscle
48	chr1:227956000-227962000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:227956000-227964200	Weak transcription	Fetal Kidney	kidney
50	chr1:227956000-227964600	Strong transcription	Sigmoid Colon	Sigmoid Colon

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