Variant report

Variant	rs2115938
Chromosome Location	chr3:141598951-141598952
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141598824..141601201-chr3:141604950..141607021,4	MCF-7	breast:
2	chr3:141455463..141459614-chr3:141593520..141599146,20	K562	blood:
3	chr3:141457377..141459578-chr3:141597906..141599752,2	MCF-7	breast:
4	chr3:141452499..141459593-chr3:141591792..141599045,17	MCF-7	breast:
5	chr3:141471164..141473196-chr3:141598108..141600224,2	K562	blood:

Variant related genes	Relation type
ENSG00000114125	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11915071	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11926859	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2068231	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28454329	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28463227	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4511872	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58370035	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6440048	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]
rs6767100	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6773662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6782993	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6801868	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804938	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805115	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806440	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73230628	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7616510	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7624456	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7642890	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648330	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849347	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9853609	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3333253	chr3:141585303-141602936	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2115938	ATP1B3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141594400-141600400	Active TSS	GM12878-XiMat	blood
2	chr3:141596400-141609400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:141596400-141626400	Weak transcription	Pancreas	Pancrea
4	chr3:141597000-141600400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:141597000-141604600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:141597000-141613200	Weak transcription	Placenta	Placenta
7	chr3:141597000-141615800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:141597000-141625200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:141597000-141646400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:141597200-141600200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:141597200-141600200	Weak transcription	Primary T cells from cord blood	blood
12	chr3:141597200-141625800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:141597400-141618800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:141597400-141618800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:141597600-141599600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:141597800-141599000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:141597800-141599200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:141597800-141600200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:141597800-141600400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr3:141597800-141600400	Weak transcription	Adipose Nuclei	Adipose
21	chr3:141597800-141601400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:141597800-141601600	Weak transcription	Fetal Stomach	stomach
23	chr3:141597800-141604200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:141597800-141606000	Weak transcription	Aorta	Aorta
25	chr3:141597800-141615800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:141597800-141617200	Weak transcription	Primary B cells from cord blood	blood
27	chr3:141597800-141617400	Weak transcription	HSMM	muscle
28	chr3:141597800-141619000	Weak transcription	Lung	lung
29	chr3:141597800-141627000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:141598000-141599000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:141598000-141599000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:141598000-141599000	Enhancers	NHDF-Ad	bronchial
33	chr3:141598000-141599400	Active TSS	HMEC	breast
34	chr3:141598000-141600200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr3:141598000-141600200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:141598000-141600200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:141598000-141600200	Weak transcription	Brain Germinal Matrix	brain
38	chr3:141598000-141600200	Weak transcription	Thymus	Thymus
39	chr3:141598000-141600400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:141598000-141600400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:141598000-141601600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:141598000-141605600	Weak transcription	HSMMtube	muscle
43	chr3:141598000-141613800	Weak transcription	Fetal Lung	lung
44	chr3:141598000-141615800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:141598000-141618600	Weak transcription	Fetal Intestine Large	intestine
46	chr3:141598000-141618800	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:141598000-141619200	Weak transcription	Psoas Muscle	Psoas
48	chr3:141598000-141625400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:141598000-141626000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:141598000-141627000	Weak transcription	Brain Hippocampus Middle	brain

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