Variant report

Variant	rs4363812
Chromosome Location	chr15:56390186-56390187
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56389724..56392498-chr15:56393728..56396342,2	K562	blood:
2	chr15:56389724..56392748-chr15:56393728..56397126,3	K562	blood:
3	chr15:56386726..56388923-chr15:56388990..56391326,2	MCF-7	breast:

Extended variants
information (count: 123 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1031077	1.00[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10518839	0.90[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.87[YRI][hapmap];0.82[ASN][1000 genomes]
rs10518842	0.82[ASN][1000 genomes]
rs10518843	0.90[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.87[YRI][hapmap];0.82[ASN][1000 genomes]
rs10851601	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10851603	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11071245	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11071246	0.86[ASN][1000 genomes]
rs11071250	0.84[ASN][1000 genomes]
rs11071252	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11071253	0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap]
rs11071254	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11629674	0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.80[ASN][1000 genomes]
rs11631518	0.90[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs11632023	0.80[ASN][1000 genomes]
rs11632087	0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap]
rs11632091	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs11634404	0.89[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.89[ASN][1000 genomes]
rs11634455	0.82[ASN][1000 genomes]
rs11636040	0.81[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs11637507	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11637789	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11638709	0.82[ASN][1000 genomes]
rs12437864	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12439682	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12439907	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12440142	0.81[EUR][1000 genomes]
rs12442539	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12443118	0.91[ASN][1000 genomes]
rs12443429	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12591236	0.81[ASN][1000 genomes]
rs12591270	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12591294	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12591980	0.82[ASN][1000 genomes]
rs12592096	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12592130	0.80[ASN][1000 genomes]
rs12592449	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12593569	0.86[CHB][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];0.87[YRI][hapmap]
rs12593752	0.82[ASN][1000 genomes]
rs12594103	0.80[ASN][1000 genomes]
rs12594245	0.82[ASN][1000 genomes]
rs12594860	0.82[ASN][1000 genomes]
rs12594908	0.81[ASN][1000 genomes]
rs12594941	0.86[CHB][hapmap];0.87[YRI][hapmap]
rs12595072	0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.89[ASN][1000 genomes]
rs12595366	0.80[ASN][1000 genomes]
rs12595557	0.90[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap]
rs12595649	0.82[ASN][1000 genomes]
rs12595840	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1550586	0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs16976734	0.81[CHD][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap]
rs16976760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16976788	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16976792	0.82[ASN][1000 genomes]
rs16976801	0.82[ASN][1000 genomes]
rs16976810	0.82[ASN][1000 genomes]
rs16976821	0.82[ASN][1000 genomes]
rs16976826	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16976847	0.85[CHB][hapmap];0.87[YRI][hapmap]
rs17841131	0.82[ASN][1000 genomes]
rs1867089	0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.80[ASN][1000 genomes]
rs1879344	0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.82[ASN][1000 genomes]
rs1879345	0.82[ASN][1000 genomes]
rs1879347	0.90[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.87[YRI][hapmap];0.82[ASN][1000 genomes]
rs1879348	0.91[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1879349	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs2682045	0.82[JPT][hapmap]
rs2718930	0.94[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs2899596	0.82[ASN][1000 genomes]
rs2899597	0.82[ASN][1000 genomes]
rs34383693	0.89[ASN][1000 genomes]
rs34401800	0.80[ASN][1000 genomes]
rs35371323	0.86[ASN][1000 genomes]
rs3803459	0.94[ASN][1000 genomes]
rs4142481	0.95[ASN][1000 genomes]
rs55946012	0.87[ASN][1000 genomes]
rs56156930	0.82[ASN][1000 genomes]
rs58036957	0.89[ASN][1000 genomes]
rs58265497	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59025920	0.89[ASN][1000 genomes]
rs59230019	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60210425	0.82[ASN][1000 genomes]
rs60417530	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61072507	0.88[ASN][1000 genomes]
rs61373424	0.95[ASN][1000 genomes]
rs61466134	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61500930	0.82[ASN][1000 genomes]
rs66670902	0.87[ASN][1000 genomes]
rs68127612	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68187092	0.94[ASN][1000 genomes]
rs72736464	0.86[ASN][1000 genomes]
rs72736479	0.92[ASN][1000 genomes]
rs72736495	0.89[ASN][1000 genomes]
rs72736498	0.89[ASN][1000 genomes]
rs72738604	0.85[ASN][1000 genomes]
rs72738605	0.81[ASN][1000 genomes]
rs72738607	0.85[ASN][1000 genomes]
rs72738608	0.83[ASN][1000 genomes]
rs72738615	0.83[ASN][1000 genomes]
rs72738616	0.80[ASN][1000 genomes]
rs72738618	0.80[ASN][1000 genomes]
rs72738620	0.83[ASN][1000 genomes]
rs72738631	0.80[ASN][1000 genomes]
rs72738638	0.82[ASN][1000 genomes]
rs72738646	0.81[ASN][1000 genomes]
rs72738648	0.82[ASN][1000 genomes]
rs72738654	0.82[ASN][1000 genomes]
rs72738656	0.82[ASN][1000 genomes]
rs72738658	0.82[ASN][1000 genomes]
rs72738659	0.82[ASN][1000 genomes]
rs72738660	0.82[ASN][1000 genomes]
rs72738662	0.82[ASN][1000 genomes]
rs72738664	0.82[ASN][1000 genomes]
rs72738666	0.82[ASN][1000 genomes]
rs72738667	0.82[ASN][1000 genomes]
rs72738668	0.82[ASN][1000 genomes]
rs72740505	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs748970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs764014	0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap]
rs8027386	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv833018	chr15:56325799-56492535	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045906	chr15:56333180-56473614	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4363812	SCG3	cis	parietal	SCAN
rs4363812	MNS1	cis	parietal	SCAN
rs4363812	UNC13C	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56381600-56391000	Strong transcription	HMEC	breast
2	chr15:56381600-56397000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:56382200-56399200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:56382600-56391000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:56382800-56395800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:56383200-56390200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:56383200-56390200	Strong transcription	Primary hematopoietic stem cells	blood
8	chr15:56383200-56395600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:56383400-56390600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:56383400-56395200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr15:56383600-56390600	Strong transcription	HSMM	muscle
12	chr15:56383600-56391000	Strong transcription	NH-A	brain
13	chr15:56383800-56390600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:56383800-56390600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:56383800-56394200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:56383800-56398400	Strong transcription	Dnd41	blood
17	chr15:56384000-56390600	Strong transcription	GM12878-XiMat	blood
18	chr15:56384000-56390800	Strong transcription	Primary B cells from cord blood	blood
19	chr15:56384000-56395800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:56384200-56391200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:56384600-56390200	Weak transcription	Stomach Mucosa	stomach
22	chr15:56384600-56390600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:56384600-56395000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:56384800-56390600	Strong transcription	Fetal Thymus	thymus
25	chr15:56385000-56390800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr15:56385000-56394000	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr15:56385000-56394800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr15:56385200-56390200	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr15:56385200-56390600	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:56385200-56391000	Strong transcription	H1 Cell Line	embryonic stem cell
31	chr15:56385400-56390200	Strong transcription	NHDF-Ad	bronchial
32	chr15:56385400-56390400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr15:56385400-56390400	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr15:56385400-56390600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr15:56385400-56390600	Strong transcription	Adipose Nuclei	Adipose
36	chr15:56385400-56390600	Strong transcription	Fetal Intestine Large	intestine
37	chr15:56385400-56390600	Strong transcription	HUVEC	blood vessel
38	chr15:56385400-56390800	Strong transcription	Primary T cells from cord blood	blood
39	chr15:56385400-56390800	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:56385400-56391000	Strong transcription	A549	lung
41	chr15:56385400-56391000	Strong transcription	HepG2	liver
42	chr15:56385600-56390200	Strong transcription	Skeletal Muscle Male	skeletal muscle
43	chr15:56385600-56390200	Strong transcription	Osteobl	bone
44	chr15:56385600-56390400	Strong transcription	Fetal Lung	lung
45	chr15:56385600-56390600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:56385600-56390600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr15:56385600-56390600	Strong transcription	Fetal Muscle Trunk	muscle
48	chr15:56385600-56390600	Strong transcription	Fetal Muscle Leg	muscle
49	chr15:56385600-56390600	Strong transcription	Left Ventricle	heart
50	chr15:56385600-56390600	Strong transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links