Variant report

Variant	rs2197208
Chromosome Location	chr3:105465404-105465405
allele	C/T
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:44)

rs_ID	r²[population]
rs10460808	0.81[EUR][1000 genomes]
rs10511246	0.81[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1075739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11921710	0.82[ASN][1000 genomes]
rs12489983	0.87[CEU][hapmap]
rs12633654	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12635232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12637560	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12637809	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639271	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1561922	0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16844736	0.81[EUR][1000 genomes]
rs16851523	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16851539	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16851563	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16851570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16851587	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16851630	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1867192	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1947000	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1992521	0.81[EUR][1000 genomes]
rs2089091	0.87[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2197209	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2301036	0.81[EUR][1000 genomes]
rs3821489	0.86[CEU][hapmap]
rs57520912	0.82[ASN][1000 genomes]
rs58340800	0.82[ASN][1000 genomes]
rs59534462	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59611997	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60295307	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60619938	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437620	0.82[ASN][1000 genomes]
rs6437621	0.82[ASN][1000 genomes]
rs73854891	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73854894	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73857222	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7624400	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7629357	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs7648842	0.82[ASN][1000 genomes]
rs9631436	0.82[ASN][1000 genomes]
rs9789988	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9826886	0.82[ASN][1000 genomes]
rs9846534	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs9874600	0.87[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv591242	chr3:105373836-105470134	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	nsv591243	chr3:105438320-105470134	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
8	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
9	nsv591245	chr3:105438806-105469882	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
10	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
11	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
rs2197208	CBLB	cis	cerebellum	SCAN
rs2197208	POU3F2	trans	brain	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105389200-105467200	Weak transcription	Stomach Mucosa	stomach
2	chr3:105433600-105465600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:105439000-105465800	Weak transcription	NHLF	lung
4	chr3:105439000-105466200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:105439000-105466600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:105439000-105471200	Weak transcription	Fetal Thymus	thymus
7	chr3:105439000-105471400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:105439000-105471400	Weak transcription	HMEC	breast
9	chr3:105439000-105471600	Weak transcription	Fetal Brain Male	brain
10	chr3:105439000-105475800	Weak transcription	Esophagus	oesophagus
11	chr3:105439000-105477400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:105439000-105477400	Weak transcription	Lung	lung
13	chr3:105439000-105477400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:105439200-105465600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:105439200-105465600	Weak transcription	Right Ventricle	heart
16	chr3:105439200-105465600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:105439200-105477200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:105445800-105465600	Weak transcription	Gastric	stomach
19	chr3:105446600-105477600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:105452400-105477400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:105452800-105477400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:105458000-105475600	Weak transcription	Pancreas	Pancrea
23	chr3:105460200-105471600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:105460800-105466000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr3:105462000-105470200	Weak transcription	Dnd41	blood
26	chr3:105463200-105465600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:105463200-105471400	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr3:105463400-105470800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:105464200-105465600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:105464200-105465800	Enhancers	Primary T cells fromperipheralblood	blood
31	chr3:105464200-105471000	Enhancers	Primary T cells from cord blood	blood
32	chr3:105464200-105477400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr3:105464200-105478200	Weak transcription	Right Atrium	heart
34	chr3:105464400-105465800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr3:105464400-105466400	Enhancers	NHEK	skin
36	chr3:105464400-105477400	Weak transcription	Fetal Lung	lung
37	chr3:105464600-105465600	Weak transcription	NH-A	brain
38	chr3:105464600-105465800	Genic enhancers	Primary B cells from cord blood	blood
39	chr3:105464600-105465800	Enhancers	Small Intestine	intestine
40	chr3:105464600-105466000	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr3:105464600-105466400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:105464600-105466400	Enhancers	Fetal Intestine Small	intestine
43	chr3:105464600-105466600	Enhancers	Primary hematopoietic stem cells	blood
44	chr3:105464600-105467600	Enhancers	Brain Hippocampus Middle	brain
45	chr3:105464600-105471200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:105464600-105477400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:105464800-105465600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:105464800-105465600	Weak transcription	GM12878-XiMat	blood
49	chr3:105464800-105465600	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr3:105464800-105465800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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