Variant report

Variant	rs745966
Chromosome Location	chr3:141653126-141653127
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141646387..141648492-chr3:141652894..141655843,2	K562	blood:
2	chr3:141651453..141653933-chr3:141655260..141657163,2	K562	blood:
3	chr3:141645508..141649980-chr3:141650119..141655905,6	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10755098	0.88[CHB][hapmap]
rs10935439	0.83[AFR][1000 genomes]
rs10935440	0.83[AFR][1000 genomes]
rs10935441	0.83[AFR][1000 genomes]
rs10935442	0.88[CHB][hapmap]
rs10935443	0.88[CHB][hapmap]
rs10935445	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10935446	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10935447	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11569190	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs11569193	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11569201	0.85[CEU][hapmap]
rs11569202	0.85[CEU][hapmap]
rs11569205	0.85[CEU][hapmap]
rs11569206	0.85[CEU][hapmap]
rs11569208	0.85[CEU][hapmap]
rs11569209	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11569218	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11569220	0.85[CEU][hapmap]
rs11569222	0.85[CEU][hapmap]
rs11569223	0.85[CEU][hapmap]
rs11569259	0.89[EUR][1000 genomes]
rs11569262	0.89[EUR][1000 genomes]
rs11569278	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11569281	0.93[EUR][1000 genomes]
rs11569291	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs11706402	0.85[CEU][hapmap]
rs11706728	1.00[ASW][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs11707100	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11707427	0.83[AFR][1000 genomes]
rs11708301	0.82[CEU][hapmap]
rs11711748	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11713023	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11716148	0.85[CEU][hapmap]
rs11717517	0.85[CEU][hapmap]
rs11718167	0.85[CEU][hapmap]
rs11719793	0.85[CEU][hapmap]
rs11721024	0.85[CHB][hapmap]
rs11844	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12487977	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12487983	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12490893	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12493472	0.85[CEU][hapmap]
rs12493495	0.85[CEU][hapmap]
rs12493643	0.85[CEU][hapmap]
rs12494971	1.00[ASW][hapmap];0.85[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];1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12497112	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12497443	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16851892	0.88[CHB][hapmap]
rs1808584	0.93[ASN][1000 genomes]
rs2115935	0.88[CHB][hapmap]
rs2288634	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2288635	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2288636	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34071952	0.83[AFR][1000 genomes]
rs3762726	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3792411	0.88[CHB][hapmap]
rs3804772	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3804773	0.88[CHB][hapmap]
rs3828398	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4683412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683413	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs4683414	0.89[EUR][1000 genomes]
rs4683418	0.85[CEU][hapmap]
rs4683638	0.83[AFR][1000 genomes]
rs4683639	0.88[CHB][hapmap]
rs4683641	0.88[CHB][hapmap]
rs4683649	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4683651	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4683652	0.92[EUR][1000 genomes]
rs4683659	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4683669	1.00[GIH][hapmap]
rs56174413	0.90[ASN][1000 genomes]
rs59122181	0.83[AFR][1000 genomes]

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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs745966	ATP1B3	cis	multi-tissue	Pritchard
rs745966	ZBTB38	cis	parietal	SCAN
rs745966	TFDP2	Cis_1M	lymphoblastoid	RTeQTL
rs745966	ATP1B3	cis	lymphoblastoid	seeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141621000-141670800	Weak transcription	Small Intestine	intestine
2	chr3:141625600-141668400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr3:141626600-141659000	Weak transcription	Pancreas	Pancrea
4	chr3:141628200-141673600	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:141628600-141658800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:141628600-141669000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:141628800-141669800	Weak transcription	Fetal Lung	lung
8	chr3:141628800-141674000	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
10	chr3:141632400-141654000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:141633000-141659000	Weak transcription	NHLF	lung
12	chr3:141634200-141682000	Weak transcription	Brain Angular Gyrus	brain
13	chr3:141634400-141656600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:141637400-141658800	Weak transcription	Brain Germinal Matrix	brain
15	chr3:141640600-141656400	Weak transcription	Fetal Brain Male	brain
16	chr3:141640600-141658800	Weak transcription	Fetal Heart	heart
17	chr3:141640800-141659200	Weak transcription	Colonic Mucosa	Colon
18	chr3:141640800-141659200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:141642800-141658600	Weak transcription	A549	lung
20	chr3:141643000-141656400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:141643000-141656400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:141643000-141675800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:141643400-141671200	Weak transcription	Right Ventricle	heart
24	chr3:141644800-141658600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:141644800-141658600	Weak transcription	NHDF-Ad	bronchial
26	chr3:141644800-141678400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:141646800-141656400	Weak transcription	K562	blood
28	chr3:141646800-141659000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:141646800-141668200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:141647000-141656200	Weak transcription	HMEC	breast
31	chr3:141647000-141656400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:141647000-141656400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr3:141647000-141668400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:141647000-141669200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr3:141647200-141656400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:141647200-141656400	Weak transcription	NHEK	skin
37	chr3:141647200-141656600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:141647200-141658800	Weak transcription	NH-A	brain
39	chr3:141647200-141659000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:141647200-141669400	Weak transcription	Primary B cells from cord blood	blood
41	chr3:141647400-141656400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:141647400-141658600	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr3:141647400-141658800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:141647400-141658800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr3:141647400-141668200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:141647400-141670400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:141647600-141658600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:141647600-141659200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr3:141647600-141670600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:141647800-141656400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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