Variant report

Variant	rs10916203
Chromosome Location	chr1:227949612-227949613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227668951..227669884-chr1:227949577..227950975,4	MCF-7	breast:
2	chr1:227946182..227953403-chr1:228132950..228136592,12	MCF-7	breast:
3	chr1:227945386..227947892-chr1:227948405..227951247,3	MCF-7	breast:
4	chr1:227924939..227926521-chr1:227948276..227949805,2	MCF-7	breast:
5	chr1:227948959..227950844-chr1:228133923..228134938,14	MCF-7	breast:
6	chr1:227913567..227919162-chr1:227947935..227954215,6	MCF-7	breast:
7	chr1:227932601..227934786-chr1:227948065..227950535,2	MCF-7	breast:
8	chr1:227948352..227950485-chr1:227952945..227955700,2	MCF-7	breast:
9	chr1:227948805..227951027-chr1:227953567..227955861,2	MCF-7	breast:
10	chr1:227948596..227951213-chr1:228129640..228131293,2	MCF-7	breast:
11	chr1:227948253..227951244-chr1:228133555..228136345,5	MCF-7	breast:
12	chr1:227938992..227942354-chr1:227946217..227950282,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143740	Chromatin interaction
ENSG00000143816	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1056699	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1060295	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799430	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs10799439	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10799447	0.89[CEU][hapmap];0.80[TSI][hapmap]
rs10799448	0.85[CEU][hapmap]
rs10916171	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs10916188	0.83[EUR][1000 genomes]
rs10916191	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10916207	0.89[CEU][hapmap];0.80[TSI][hapmap]
rs1111046	0.96[CEU][hapmap];0.93[CHB][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1155807	0.89[CEU][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12025942	0.85[CEU][hapmap]
rs12033610	0.82[CEU][hapmap];0.84[TSI][hapmap]
rs1810680	0.89[CEU][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1923823	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2104245	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2236360	0.92[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2236361	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4500311	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4653856	0.84[CEU][hapmap];0.80[JPT][hapmap]
rs6426468	0.89[CEU][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6426473	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6660432	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6693054	0.89[CEU][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6703846	0.89[CEU][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs730684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7522634	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7526184	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533588	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534403	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7536765	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7539282	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552193	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9786978	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9969994	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10916203	ZNF678	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227924200-227955000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:227934400-227950000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:227934800-227950200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:227934800-227950400	Strong transcription	Fetal Intestine Small	intestine
5	chr1:227935200-227949800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:227938000-227950200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:227938600-227950400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:227940400-227950000	Strong transcription	HepG2	liver
9	chr1:227940800-227949800	Strong transcription	Thymus	Thymus
10	chr1:227942000-227950000	Weak transcription	Small Intestine	intestine
11	chr1:227942600-227950000	Weak transcription	Stomach Mucosa	stomach
12	chr1:227943400-227949800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:227943600-227949800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:227943600-227949800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:227944000-227949800	Strong transcription	Brain Germinal Matrix	brain
16	chr1:227944000-227950400	Strong transcription	Fetal Intestine Large	intestine
17	chr1:227944000-227951800	Genic enhancers	Fetal Muscle Leg	muscle
18	chr1:227944200-227950000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:227944600-227949800	Weak transcription	Hela-S3	cervix
20	chr1:227945000-227949800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr1:227945800-227949800	Strong transcription	Aorta	Aorta
22	chr1:227945800-227954800	Weak transcription	Fetal Kidney	kidney
23	chr1:227946000-227949800	Strong transcription	Brain Hippocampus Middle	brain
24	chr1:227946000-227950600	Genic enhancers	GM12878-XiMat	blood
25	chr1:227946000-227960400	Strong transcription	Fetal Brain Female	brain
26	chr1:227946200-227950000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:227946400-227950000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:227946400-227950000	Strong transcription	Fetal Lung	lung
29	chr1:227946400-227950000	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:227946600-227950000	Strong transcription	Lung	lung
31	chr1:227946800-227950000	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:227946800-227952400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:227947000-227949800	Strong transcription	Pancreas	Pancrea
34	chr1:227947600-227949800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr1:227947600-227949800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:227947600-227954800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:227947800-227949800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr1:227947800-227949800	Genic enhancers	HSMM	muscle
39	chr1:227947800-227949800	Strong transcription	NHEK	skin
40	chr1:227947800-227950000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:227947800-227950200	Strong transcription	Ovary	ovary
42	chr1:227947800-227950400	Weak transcription	HUVEC	blood vessel
43	chr1:227947800-227951600	Enhancers	Fetal Heart	heart
44	chr1:227947800-227955400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:227948000-227950400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:227948000-227950400	Strong transcription	Fetal Stomach	stomach
47	chr1:227948000-227953600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:227948200-227952200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
49	chr1:227948200-227954600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:227948400-227949800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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