Variant report

Variant	rs6440048
Chromosome Location	chr3:141622055-141622056
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:141622032-141622387	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:141621884-141622086	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:141594674..141598943-chr3:141621711..141625603,5	MCF-7	breast:
2	chr3:141594460..141597483-chr3:141621419..141624479,3	K562	blood:
3	chr3:141593925..141596999-chr3:141621116..141624479,3	K562	blood:

Variant related genes	Relation type
RNU6-509P	TF binding region
ATP1B3	TF binding region
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11915071	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11926859	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2068231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115938	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28454329	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28463227	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4511872	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58370035	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767100	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6773662	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6782694	0.93[TSI][hapmap]
rs6782993	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801868	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6804938	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6805115	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6806440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230628	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7616510	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7624456	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7642890	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7648330	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9849347	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9853609	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6440048	ATP1B3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141596400-141626400	Weak transcription	Pancreas	Pancrea
2	chr3:141597000-141625200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:141597000-141646400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:141597200-141625800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:141597800-141627000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:141598000-141625400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:141598000-141626000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:141598000-141627000	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:141598000-141627200	Weak transcription	Colonic Mucosa	Colon
10	chr3:141598000-141642000	Weak transcription	Right Ventricle	heart
11	chr3:141598200-141626000	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:141598200-141627200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:141598200-141640200	Weak transcription	Fetal Brain Male	brain
14	chr3:141598200-141640200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:141598400-141622200	Weak transcription	Left Ventricle	heart
16	chr3:141598400-141623800	Weak transcription	NH-A	brain
17	chr3:141605200-141627200	Weak transcription	Primary T cells from cord blood	blood
18	chr3:141606200-141623600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:141606800-141625200	Weak transcription	HSMMtube	muscle
20	chr3:141607200-141623800	Weak transcription	HUVEC	blood vessel
21	chr3:141614000-141626000	Weak transcription	Fetal Lung	lung
22	chr3:141614200-141624000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:141614800-141625200	Weak transcription	NHDF-Ad	bronchial
24	chr3:141615000-141622200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:141616200-141623600	Weak transcription	Aorta	Aorta
26	chr3:141616200-141623800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:141616200-141625800	Weak transcription	NHLF	lung
28	chr3:141616200-141627000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:141616200-141646600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:141616200-141648600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:141616400-141622800	Weak transcription	HepG2	liver
32	chr3:141616400-141623800	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:141616400-141626000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:141616800-141627200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:141617800-141622400	Weak transcription	Hela-S3	cervix
36	chr3:141618000-141633600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr3:141618400-141622400	Weak transcription	K562	blood
38	chr3:141618400-141623800	Weak transcription	HSMM	muscle
39	chr3:141619200-141622400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:141619200-141622400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:141619200-141625800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:141619400-141622200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:141619400-141624000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:141619400-141624200	Weak transcription	HMEC	breast
45	chr3:141619400-141625200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:141619400-141625200	Weak transcription	Adipose Nuclei	Adipose
47	chr3:141619400-141625400	Weak transcription	Primary B cells from cord blood	blood
48	chr3:141619400-141625400	Weak transcription	Fetal Brain Female	brain
49	chr3:141619400-141626400	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:141619400-141627200	Weak transcription	Brain Germinal Matrix	brain

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