Variant report

Variant	rs13060223
Chromosome Location	chr3:105495841-105495842
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10804442	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933833	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11711088	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12636287	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13085563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13100446	0.93[AMR][1000 genomes]
rs1443102	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1470283	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1550711	1.00[ASW][hapmap]
rs1867191	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs1867195	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1992522	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2055557	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2099892	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2120105	0.83[ASW][hapmap];0.80[GIH][hapmap]
rs2399056	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427229	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28533328	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3996189	0.87[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4243427	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4447799	0.93[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4894950	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894953	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894954	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4894957	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4894960	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4894962	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6437624	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6788366	0.87[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6795961	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6807382	0.87[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs71627856	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs726443	1.00[ASW][hapmap]
rs7432372	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7637327	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7645021	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7647955	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7651784	1.00[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs769315	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs971110	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9841500	1.00[ASW][hapmap];0.87[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877306	chr3:105372196-105495841	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv877308	chr3:105373836-105495841	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv877310	chr3:105409321-105495841	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv591244	chr3:105438320-105495841	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv591246	chr3:105439522-105504129	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13060223	CBLB	cis	cerebellum	SCAN
rs13060223	ALCAM	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105467600-105509400	Weak transcription	Stomach Mucosa	stomach
2	chr3:105472200-105499000	Weak transcription	NHDF-Ad	bronchial
3	chr3:105472400-105504400	Weak transcription	HUVEC	blood vessel
4	chr3:105478600-105509400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:105478600-105511200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:105478800-105496200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:105481200-105500800	Weak transcription	Small Intestine	intestine
8	chr3:105481400-105509600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:105481600-105498000	Weak transcription	NH-A	brain
10	chr3:105481800-105507400	Weak transcription	HSMM	muscle
11	chr3:105482000-105496200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:105482000-105496200	Weak transcription	Lung	lung
13	chr3:105482000-105503800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:105482000-105509200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:105482000-105509600	Weak transcription	Ovary	ovary
16	chr3:105482000-105510800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:105482000-105511200	Weak transcription	Aorta	Aorta
18	chr3:105482400-105500000	Weak transcription	Fetal Stomach	stomach
19	chr3:105482800-105517400	Weak transcription	Fetal Intestine Large	intestine
20	chr3:105483200-105506200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
22	chr3:105486800-105519000	Weak transcription	Esophagus	oesophagus
23	chr3:105487000-105497400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:105487000-105508400	Weak transcription	Fetal Lung	lung
25	chr3:105487200-105508400	Weak transcription	Fetal Kidney	kidney
26	chr3:105487400-105500600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:105487400-105504200	Weak transcription	Fetal Heart	heart
28	chr3:105489400-105506000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:105489600-105509600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:105489600-105525400	Weak transcription	Fetal Intestine Small	intestine
31	chr3:105489800-105496000	Weak transcription	Right Ventricle	heart
32	chr3:105493000-105501400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr3:105493000-105501400	Weak transcription	Left Ventricle	heart
34	chr3:105493000-105502400	Weak transcription	Brain Anterior Caudate	brain
35	chr3:105493000-105511200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:105493000-105511200	Weak transcription	Right Atrium	heart
37	chr3:105493200-105501400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:105493200-105509000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:105493400-105496400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:105494000-105506200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr3:105494400-105509400	Weak transcription	Primary B cells from cord blood	blood
42	chr3:105494400-105516200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:105494800-105496000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:105494800-105496200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:105494800-105496200	Weak transcription	Gastric	stomach
46	chr3:105494800-105500000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr3:105494800-105500800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:105495000-105500800	Weak transcription	Primary T cells from cord blood	blood
49	chr3:105495000-105509600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:105495200-105496400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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