Variant report

Variant	rs3976787
Chromosome Location	chr18:12971894-12971895
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:12971689-12971907	K562	blood:	n/a	n/a
2	POLR2A	chr18:12971682-12972862	HepG2	liver:	n/a	n/a
3	POLR2A	chr18:12971847-12972478	GM12878	blood:	n/a	n/a
4	POLR2A	chr18:12971827-12972128	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:12946986..12949410-chr18:12970714..12972312,2	MCF-7	breast:
2	chr18:12971249..12974224-chr18:12989349..12991861,2	MCF-7	breast:
3	chr18:12948345..12951130-chr18:12969418..12973863,3	K562	blood:
4	chr18:12969942..12972168-chr18:12978134..12980197,2	K562	blood:

Variant related genes	Relation type
SEH1L	TF binding region
ENSG00000085415	Chromatin interaction
ENSG00000101639	Chromatin interaction
ENSG00000266969	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10163827	0.91[ASN][1000 genomes]
rs11080617	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11080618	0.84[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11661908	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11662634	0.91[ASN][1000 genomes]
rs11662766	0.87[JPT][hapmap]
rs11664213	0.97[ASN][1000 genomes]
rs11664469	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs12604538	0.81[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap]
rs12605267	0.99[ASN][1000 genomes]
rs12607398	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12607919	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12953783	0.89[ASN][1000 genomes]
rs12957380	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs12960349	0.84[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12961596	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963426	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12967249	0.80[AMR][1000 genomes]
rs12970503	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13381779	0.91[ASN][1000 genomes]
rs1523064	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17603207	0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17659689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17659749	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17659896	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.97[ASN][1000 genomes]
rs2015763	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2282540	0.87[ASN][1000 genomes]
rs2282541	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.90[ASN][1000 genomes]
rs28551661	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28654613	0.96[ASN][1000 genomes]
rs34166083	0.97[ASN][1000 genomes]
rs34302481	0.97[ASN][1000 genomes]
rs35368962	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35563947	0.97[ASN][1000 genomes]
rs3809914	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4499304	0.92[CEU][hapmap]
rs56263236	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6505772	0.87[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap]
rs68004799	0.97[ASN][1000 genomes]
rs7227812	0.85[MKK][hapmap]
rs7228684	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.95[ASN][1000 genomes]
rs7229406	0.87[CHB][hapmap]
rs7229869	0.84[ASN][1000 genomes]
rs7230391	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7230435	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7234163	0.92[CEU][hapmap]
rs7234938	0.87[ASN][1000 genomes]
rs7236710	0.81[ASN][1000 genomes]
rs7237711	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7239486	0.90[ASN][1000 genomes]
rs8083393	0.86[JPT][hapmap]
rs8083401	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8086882	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8089724	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8090667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8092888	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8093236	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8093576	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8096860	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8566	0.97[ASN][1000 genomes]
rs9950241	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1057083	chr18:12916779-13207538	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv576524	chr18:12918318-13183609	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1056593	chr18:12926314-13183383	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1064364	chr18:12926314-13207686	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3976787	CEP192	cis	Esophagus Muscularis	GTEx
rs3976787	CEP192	cis	Thyroid	GTEx
rs3976787	CEP192	cis	cerebellum	SCAN
rs3976787	CEP192	cis	parietal	SCAN
rs3976787	CEP192	cis	Artery Tibial	GTEx
rs3976787	CEP192	cis	Nerve Tibial	GTEx
rs3976787	CEP192	cis	lung	GTEx
rs3976787	CEP192	Cis_1M	lymphoblastoid	RTeQTL
rs3976787	CEP192	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12948800-12976600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr18:12948800-12989000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr18:12949000-12975400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr18:12949200-12972000	Weak transcription	Right Ventricle	heart
5	chr18:12949200-12989400	Weak transcription	Psoas Muscle	Psoas
6	chr18:12950000-12990200	Weak transcription	Fetal Brain Male	brain
7	chr18:12951400-12990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr18:12951600-12988200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr18:12951800-12978400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr18:12953200-12979000	Strong transcription	Fetal Thymus	thymus
11	chr18:12956200-12975800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr18:12957400-12978400	Strong transcription	Dnd41	blood
13	chr18:12959000-12972000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr18:12959000-12990200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr18:12959200-12978200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:12960400-12972400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr18:12961000-12978400	Strong transcription	Fetal Intestine Small	intestine
18	chr18:12961200-12975400	Weak transcription	Stomach Mucosa	stomach
19	chr18:12961400-12975600	Weak transcription	Right Atrium	heart
20	chr18:12961600-12975400	Weak transcription	Fetal Heart	heart
21	chr18:12962200-12974000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr18:12962800-12975800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr18:12963200-12978600	Strong transcription	Fetal Intestine Large	intestine
24	chr18:12963600-12978600	Strong transcription	Fetal Stomach	stomach
25	chr18:12964000-12972000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr18:12964000-12972200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr18:12964000-12975400	Weak transcription	Colonic Mucosa	Colon
28	chr18:12964200-12972000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr18:12965000-12972000	Weak transcription	Esophagus	oesophagus
30	chr18:12966600-12973200	Strong transcription	NHEK	skin
31	chr18:12968400-12972000	Weak transcription	Left Ventricle	heart
32	chr18:12968600-12983000	Weak transcription	HUVEC	blood vessel
33	chr18:12968800-12972600	Weak transcription	Colon Smooth Muscle	Colon
34	chr18:12969400-12976000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr18:12969800-12979000	Strong transcription	Primary B cells from cord blood	blood
36	chr18:12969800-12979000	Strong transcription	Osteobl	bone
37	chr18:12970000-12972800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr18:12970000-12979000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr18:12970000-12979000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr18:12970200-12973000	Strong transcription	NH-A	brain
41	chr18:12970200-12976600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr18:12970200-12976600	Strong transcription	K562	blood
43	chr18:12970200-12976800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr18:12970200-12978200	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr18:12970200-12978600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr18:12970200-12978800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr18:12970200-12978800	Strong transcription	Liver	Liver
48	chr18:12970200-12979000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr18:12970200-12979000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr18:12970400-12975800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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