Variant report

Variant	rs4773857
Chromosome Location	chr13:95884048-95884049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11616679	0.89[GIH][hapmap]
rs12428470	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12854605	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1678400	0.85[ASN][1000 genomes]
rs1678403	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1824911	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1824912	0.87[AMR][1000 genomes]
rs1824913	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1926656	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1926657	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2389203	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2766476	0.95[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2892707	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2892713	0.91[GIH][hapmap]
rs3782963	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3782965	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3782966	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3782968	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4148440	0.89[GIH][hapmap]
rs4148455	0.83[CHB][hapmap];0.92[GIH][hapmap]
rs4148463	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4148464	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4148465	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4148467	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4148469	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4148470	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4148471	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4238313	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4303338	1.00[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4334136	0.93[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4371040	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4505186	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4520712	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4612933	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4636781	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4771907	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4771908	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4773847	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4773848	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4773849	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4773853	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4773854	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4773855	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6492769	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6492771	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7139533	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7321623	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7321744	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7322825	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7324706	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7325019	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7329432	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7330776	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7332663	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7333234	0.85[CEU][hapmap];0.83[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7333281	0.95[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7335147	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7335233	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7983336	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7987653	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7988494	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7999175	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs899494	1.00[CEU][hapmap]
rs899495	0.95[CHB][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap]
rs899496	0.92[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs899497	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs943288	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9516537	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9516538	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9516539	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9516545	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9524828	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9524830	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9524831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9524833	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9524835	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9524836	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9524840	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9524845	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9524848	0.95[CHB][hapmap];0.92[ASN][1000 genomes]
rs9524850	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9524856	0.85[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533659	chr13:95757713-96042149	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv832689	chr13:95759073-95921308	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4773857	GPC5	cis	parietal	SCAN
rs4773857	HS6ST3	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95842200-95898200	Weak transcription	NHDF-Ad	bronchial
2	chr13:95856400-95898200	Weak transcription	NHEK	skin
3	chr13:95859000-95885800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr13:95859000-95887800	Weak transcription	HSMM	muscle
5	chr13:95859000-95901000	Weak transcription	Aorta	Aorta
6	chr13:95859200-95901400	Weak transcription	Primary T cells from cord blood	blood
7	chr13:95859200-95902200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr13:95861600-95906200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:95861800-95899000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr13:95862000-95898200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr13:95862200-95898200	Weak transcription	HSMMtube	muscle
12	chr13:95863000-95898400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr13:95863200-95895400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr13:95866200-95887600	Weak transcription	HUVEC	blood vessel
15	chr13:95866200-95897400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr13:95866200-95897600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr13:95872000-95897600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:95872200-95897400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr13:95874800-95888200	Weak transcription	NHLF	lung
20	chr13:95874800-95897800	Weak transcription	Pancreas	Pancrea
21	chr13:95874800-95898200	Weak transcription	Colonic Mucosa	Colon
22	chr13:95875000-95897600	Weak transcription	Fetal Intestine Large	intestine
23	chr13:95879200-95887600	Weak transcription	Gastric	stomach
24	chr13:95879200-95907400	Weak transcription	Small Intestine	intestine
25	chr13:95879200-95914000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr13:95879400-95897400	Weak transcription	Fetal Intestine Small	intestine
27	chr13:95879600-95893800	Weak transcription	Duodenum Mucosa	Duodenum
28	chr13:95879600-95898200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr13:95880000-95887200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr13:95880600-95922600	Weak transcription	Psoas Muscle	Psoas
31	chr13:95880800-95885600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr13:95880800-95887800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr13:95880800-95888000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr13:95880800-95898600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr13:95880800-95902400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr13:95881600-95904000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr13:95881800-95887200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr13:95882200-95887600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr13:95882200-95898200	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr13:95882800-95885800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr13:95883200-95884800	Strong transcription	GM12878-XiMat	blood
42	chr13:95883600-95884200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr13:95883600-95884600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr13:95884000-95885800	Strong transcription	K562	blood
45	chr13:95884000-95886600	Weak transcription	A549	lung
46	chr13:95884000-95895400	Weak transcription	Lung	lung
47	chr13:95884000-95898200	Weak transcription	Stomach Smooth Muscle	stomach

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