Variant report

Variant	rs12497428
Chromosome Location	chr3:105524489-105524490
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105511734..105513345-chr3:105521951..105524573,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11919893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11926659	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12486371	0.83[CEU][hapmap]
rs12496588	0.83[CEU][hapmap]
rs12632980	1.00[CEU][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs13090949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13326550	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13433776	1.00[CEU][hapmap];0.83[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1503923	0.81[ASN][1000 genomes]
rs16851596	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16851705	0.86[ASN][1000 genomes]
rs16851706	0.83[ASN][1000 genomes]
rs2120103	0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs2120104	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2399056	0.92[CEU][hapmap]
rs6437616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6766168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776593	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778745	0.83[CEU][hapmap]
rs6780432	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6791765	0.83[CEU][hapmap]
rs7634195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638504	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7639888	0.83[CEU][hapmap]
rs894541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9811776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814582	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9837243	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846445	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849559	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9859953	0.80[ASW][hapmap]
rs9872895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876110	0.83[CEU][hapmap]
rs9880744	0.83[CEU][hapmap]

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	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
2	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12497428	CBLB	cis	cerebellum	SCAN
rs12497428	GUCA1C	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
2	chr3:105489600-105525400	Weak transcription	Fetal Intestine Small	intestine
3	chr3:105505000-105527800	Weak transcription	Pancreas	Pancrea
4	chr3:105505000-105548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:105509800-105527800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
7	chr3:105512200-105527200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:105512200-105534200	Weak transcription	Left Ventricle	heart
9	chr3:105512600-105524600	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:105512600-105525200	Weak transcription	HSMM	muscle
11	chr3:105515400-105528200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:105515400-105539000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:105517800-105524800	Weak transcription	A549	lung
14	chr3:105517800-105525400	Weak transcription	Fetal Intestine Large	intestine
15	chr3:105517800-105527800	Weak transcription	Fetal Kidney	kidney
16	chr3:105517800-105528200	Weak transcription	Brain Substantia Nigra	brain
17	chr3:105517800-105528400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:105518400-105525600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:105518400-105525800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:105519200-105541600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:105519400-105524800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:105519400-105527800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:105520600-105525200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr3:105520800-105525200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:105520800-105531400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:105521200-105525000	Weak transcription	NHDF-Ad	bronchial
27	chr3:105521200-105525800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr3:105521200-105527800	Weak transcription	Fetal Lung	lung
29	chr3:105521200-105530200	Weak transcription	HMEC	breast
30	chr3:105521200-105531200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr3:105521200-105536000	Weak transcription	Right Ventricle	heart
32	chr3:105521200-105546800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:105521400-105525400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:105521400-105528200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:105521400-105529200	Weak transcription	Psoas Muscle	Psoas
36	chr3:105521400-105530200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:105521400-105541200	Weak transcription	Fetal Muscle Leg	muscle
38	chr3:105521400-105542000	Weak transcription	Fetal Stomach	stomach
39	chr3:105521600-105528000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:105521600-105530200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr3:105521800-105525200	Weak transcription	HepG2	liver
42	chr3:105522000-105527000	Weak transcription	Primary B cells from cord blood	blood
43	chr3:105522200-105524600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr3:105522200-105524800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:105522200-105524800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr3:105522200-105528400	Weak transcription	Fetal Heart	heart
47	chr3:105522400-105525000	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:105522400-105526600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:105522400-105529800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:105522400-105533800	Weak transcription	Brain Germinal Matrix	brain

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