Variant report

Variant	rs1867191
Chromosome Location	chr3:105478852-105478853
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10804442	0.94[ASW][hapmap];0.86[YRI][hapmap]
rs11708360	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060223	1.00[ASW][hapmap];0.82[YRI][hapmap]
rs13061514	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1372982	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs1443102	0.92[YRI][hapmap]
rs1522287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1546733	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1550711	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561919	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1584028	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851440	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1992522	0.82[YRI][hapmap]
rs2010718	0.82[ASN][1000 genomes]
rs2034157	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2120105	0.83[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2289746	0.82[TSI][hapmap]
rs2293148	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2301044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2301045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2301046	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2399056	0.86[YRI][hapmap]
rs35903551	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772539	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4476538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894940	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4894944	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4894950	0.86[YRI][hapmap]
rs6437612	0.86[EUR][1000 genomes]
rs6437624	1.00[ASW][hapmap]
rs6767808	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6777124	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6787175	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6795961	1.00[ASW][hapmap];0.86[YRI][hapmap]
rs6800344	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs726443	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7612189	0.81[ASN][1000 genomes]
rs7640740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644634	0.85[EUR][1000 genomes]
rs7645026	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7646159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651784	1.00[ASW][hapmap]
rs769315	1.00[ASW][hapmap];0.86[YRI][hapmap]
rs9832882	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9841500	1.00[ASW][hapmap]
rs9873655	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9876007	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs1867191	CD47	cis	cerebellum	SCAN
rs1867191	CBLB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105464800-105482600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:105465800-105483400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:105466000-105481200	Weak transcription	Fetal Kidney	kidney
4	chr3:105466600-105481400	Weak transcription	HepG2	liver
5	chr3:105467600-105480800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:105467600-105509400	Weak transcription	Stomach Mucosa	stomach
7	chr3:105472200-105499000	Weak transcription	NHDF-Ad	bronchial
8	chr3:105472400-105504400	Weak transcription	HUVEC	blood vessel
9	chr3:105472800-105480200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:105473000-105481400	Weak transcription	NH-A	brain
11	chr3:105474600-105483200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:105475200-105483000	Strong transcription	Osteobl	bone
13	chr3:105475200-105485600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:105475800-105483000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:105476000-105486600	Weak transcription	Psoas Muscle	Psoas
16	chr3:105476200-105480400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr3:105476400-105480400	Weak transcription	Small Intestine	intestine
18	chr3:105476400-105480600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:105477000-105481200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:105477200-105479000	ZNF genes & repeats	Fetal Intestine Small	intestine
21	chr3:105477400-105479000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
22	chr3:105477400-105479000	ZNF genes & repeats	Dnd41	blood
23	chr3:105477400-105479600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
24	chr3:105477600-105479000	ZNF genes & repeats	Brain Germinal Matrix	brain
25	chr3:105477600-105479400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
26	chr3:105477600-105482800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr3:105477800-105479000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:105477800-105486800	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:105478000-105480400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr3:105478000-105481200	Weak transcription	Brain Substantia Nigra	brain
31	chr3:105478200-105495400	Weak transcription	HSMMtube	muscle
32	chr3:105478400-105479000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:105478400-105479000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr3:105478400-105479400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:105478400-105481000	Weak transcription	Adipose Nuclei	Adipose
36	chr3:105478400-105481200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:105478400-105481200	Weak transcription	Colonic Mucosa	Colon
38	chr3:105478400-105481200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:105478600-105479800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:105478600-105479800	Weak transcription	Fetal Brain Female	brain
41	chr3:105478600-105480000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:105478600-105480400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:105478600-105480400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:105478600-105480600	Weak transcription	Fetal Lung	lung
45	chr3:105478600-105480800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:105478600-105480800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:105478600-105480800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:105478600-105481000	Weak transcription	Liver	Liver
49	chr3:105478600-105481200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:105478600-105481400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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