Variant report

Variant	rs7619647
Chromosome Location	chr3:105493286-105493287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1042852	0.92[ASW][hapmap];0.83[CEU][hapmap];0.96[GIH][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes]
rs10446294	0.84[AMR][1000 genomes]
rs10490830	0.92[CHB][hapmap];0.84[ASN][1000 genomes]
rs11706886	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11713094	0.82[AMR][1000 genomes]
rs11915926	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11929289	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486371	1.00[ASW][hapmap]
rs12493181	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12493560	0.95[YRI][hapmap];0.87[AMR][1000 genomes]
rs12695122	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12695123	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13059405	0.95[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13061160	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13062734	0.92[CHB][hapmap];0.97[CHD][hapmap];0.92[ASN][1000 genomes]
rs13064310	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs13065142	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13070917	0.85[CHB][hapmap]
rs13073784	0.90[CHB][hapmap]
rs13082334	0.85[CHB][hapmap];0.97[CHD][hapmap];0.84[ASN][1000 genomes]
rs13083716	0.88[AMR][1000 genomes]
rs13084260	0.87[CEU][hapmap];0.88[AMR][1000 genomes]
rs13093260	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13315174	0.82[AMR][1000 genomes]
rs13317635	0.92[ASW][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs1443105	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1443106	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1443108	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1530420	0.81[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1545304	0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs17202230	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17202348	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs1867189	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1867190	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2083758	0.96[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2083761	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2120585	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2244737	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2284993	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2301029	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2301030	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2301032	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2301037	0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2301040	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2301041	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2301043	1.00[ASW][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2301050	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2301051	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2305035	1.00[ASW][hapmap];0.86[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2305036	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2305037	0.91[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2399054	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2399055	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28532512	0.88[AMR][1000 genomes]
rs34520191	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34896116	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35748894	0.82[AMR][1000 genomes]
rs35834008	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3772513	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772515	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3772521	0.95[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772526	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3772527	0.95[CEU][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3772531	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3772536	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap]
rs3772537	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap]
rs3821488	0.81[CHB][hapmap];0.82[AMR][1000 genomes]
rs4321559	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4627779	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6437614	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6773661	0.95[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6796643	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726444	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7615317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7624530	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs7639888	0.92[ASW][hapmap]
rs7641825	0.85[ASW][hapmap]
rs7646445	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7649520	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652702	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs894937	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9288815	0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9657914	0.86[CEU][hapmap];0.86[AMR][1000 genomes]
rs9657915	0.88[AMR][1000 genomes]
rs9816486	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9860539	0.82[AMR][1000 genomes]
rs9870097	0.82[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9872897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9876110	0.92[ASW][hapmap]
rs9876767	0.96[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9877805	0.82[AMR][1000 genomes]
rs9878058	0.82[AMR][1000 genomes]
rs9880861	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[GIH][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs999046	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv877311	chr3:105449986-105493286	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7619647	CD47	cis	parietal	SCAN
rs7619647	CBLB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 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	chr3:105478200-105495400	Weak transcription	HSMMtube	muscle
5	chr3:105478600-105509400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:105478600-105511200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:105478800-105496200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:105481200-105500800	Weak transcription	Small Intestine	intestine
9	chr3:105481400-105509600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:105481600-105498000	Weak transcription	NH-A	brain
11	chr3:105481800-105507400	Weak transcription	HSMM	muscle
12	chr3:105482000-105496200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:105482000-105496200	Weak transcription	Lung	lung
14	chr3:105482000-105503800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:105482000-105509200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:105482000-105509600	Weak transcription	Ovary	ovary
17	chr3:105482000-105510800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:105482000-105511200	Weak transcription	Aorta	Aorta
19	chr3:105482200-105494600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:105482400-105493600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:105482400-105494400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:105482400-105500000	Weak transcription	Fetal Stomach	stomach
23	chr3:105482800-105517400	Weak transcription	Fetal Intestine Large	intestine
24	chr3:105483200-105506200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
26	chr3:105484800-105494600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:105486800-105519000	Weak transcription	Esophagus	oesophagus
28	chr3:105487000-105497400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:105487000-105508400	Weak transcription	Fetal Lung	lung
30	chr3:105487200-105508400	Weak transcription	Fetal Kidney	kidney
31	chr3:105487400-105494400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:105487400-105494800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:105487400-105500600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:105487400-105504200	Weak transcription	Fetal Heart	heart
35	chr3:105489400-105506000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:105489600-105494400	Weak transcription	Fetal Muscle Leg	muscle
37	chr3:105489600-105494800	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr3:105489600-105509600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:105489600-105525400	Weak transcription	Fetal Intestine Small	intestine
40	chr3:105489800-105495000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:105489800-105496000	Weak transcription	Right Ventricle	heart
42	chr3:105490000-105494000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:105490200-105494800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:105490600-105494800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:105490800-105494800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr3:105491200-105493600	Enhancers	Primary B cells from peripheral blood	blood
47	chr3:105491600-105495200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr3:105492200-105494600	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr3:105492400-105495600	Strong transcription	Osteobl	bone
50	chr3:105492600-105493400	Enhancers	Fetal Brain Female	brain

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