Variant report

Variant	rs1352654
Chromosome Location	chr1:151861477-151861478
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151860890..151862154-chr1:151973910..151974830,5	MCF-7	breast:
2	chr1:151861451..151862101-chr1:151985405..151986706,6	MCF-7	breast:
3	chr1:151861146..151861906-chr1:152006828..152007519,2	MCF-7	breast:
4	chr1:151858712..151862714-chr1:151863688..151869439,8	K562	blood:
5	chr1:151861047..151861926-chr1:151976278..151977205,2	MCF-7	breast:
6	chr1:151861330..151862021-chr1:151940185..151941034,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1003107	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10158030	0.90[GIH][hapmap];0.87[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1048910	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10749666	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10788813	0.86[EUR][1000 genomes]
rs10788814	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10788816	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10888448	0.85[AMR][1000 genomes]
rs10888449	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10888450	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888451	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888453	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11204905	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs11204911	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204912	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12723616	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs1387834	0.90[GIH][hapmap]
rs1387835	0.90[GIH][hapmap]
rs1490187	0.90[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs1490190	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1490191	0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1552606	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1844542	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1873310	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1873312	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2054948	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2087549	0.89[GIH][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2130526	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2171917	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2338200	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2338203	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2338204	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2338210	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932578	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2932584	0.88[ASN][1000 genomes]
rs2999529	0.90[GIH][hapmap]
rs3007682	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3007690	0.93[CHD][hapmap];0.90[GIH][hapmap]
rs3007692	0.88[ASN][1000 genomes]
rs3007700	0.90[GIH][hapmap]
rs3007704	0.93[CHD][hapmap];0.90[GIH][hapmap]
rs34370890	0.91[ASN][1000 genomes]
rs3748805	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3762427	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4551598	0.92[EUR][1000 genomes]
rs4845385	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4845388	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4845393	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4845660	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845664	1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845699	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6587626	0.90[GIH][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6587627	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6587628	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587629	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6587630	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6659029	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6662463	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6678664	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6685291	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690443	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6691350	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7529451	1.00[CHD][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7532721	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541498	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7544380	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7545863	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7552869	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs902314	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902315	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs902316	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943225	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1352654	THEM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151831000-151881400	Weak transcription	Ovary	ovary
2	chr1:151840600-151864600	Weak transcription	NH-A	brain
3	chr1:151841200-151880800	Weak transcription	NHLF	lung
4	chr1:151841600-151864000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:151844000-151864600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:151844400-151866400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:151844400-151881200	Weak transcription	Aorta	Aorta
8	chr1:151844600-151863600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:151844600-151864200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:151844800-151863800	Weak transcription	Brain Substantia Nigra	brain
11	chr1:151844800-151864200	Weak transcription	Pancreas	Pancrea
12	chr1:151844800-151870800	Weak transcription	Gastric	stomach
13	chr1:151844800-151871200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:151844800-151877600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:151845200-151863600	Weak transcription	Fetal Kidney	kidney
16	chr1:151845400-151871200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:151846000-151861800	Weak transcription	Psoas Muscle	Psoas
18	chr1:151846000-151864200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:151846400-151865400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:151846400-151870400	Weak transcription	Right Ventricle	heart
21	chr1:151846400-151871600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:151846600-151864800	Weak transcription	Fetal Lung	lung
23	chr1:151846800-151863000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:151847000-151863800	Weak transcription	Fetal Thymus	thymus
25	chr1:151847000-151865000	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr1:151847000-151869600	Weak transcription	Small Intestine	intestine
27	chr1:151847000-151871000	Weak transcription	Spleen	Spleen
28	chr1:151847400-151870600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:151847600-151862000	Weak transcription	Adipose Nuclei	Adipose
30	chr1:151847800-151864000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr1:151848000-151863000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:151848400-151863600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:151850800-151864800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:151851000-151871200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:151851200-151862000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:151854000-151880200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:151854200-151863600	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:151854200-151864800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr1:151855000-151863000	Weak transcription	Placenta	Placenta
40	chr1:151857000-151873000	Weak transcription	GM12878-XiMat	blood
41	chr1:151857600-151861600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:151857600-151864800	Weak transcription	Primary B cells from peripheral blood	blood
43	chr1:151857600-151873400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr1:151857600-151874200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr1:151857800-151866600	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:151857800-151867800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:151857800-151868400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:151858000-151863200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:151858000-151864000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr1:151858000-151866400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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