Variant report

Variant	rs16851892
Chromosome Location	chr3:141597538-141597539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141455466..141460652-chr3:141593125..141598625,15	K562	blood:
2	chr3:141594674..141598943-chr3:141621711..141625603,5	MCF-7	breast:
3	chr3:141455463..141459614-chr3:141593520..141599146,20	K562	blood:
4	chr3:141511387..141514014-chr3:141597034..141598647,2	K562	blood:
5	chr3:141452499..141459593-chr3:141591792..141599045,17	MCF-7	breast:
6	chr3:141574992..141577884-chr3:141596784..141598377,2	K562	blood:

Variant related genes	Relation type
ENSG00000114125	Chromatin interaction
ENSG00000200389	Chromatin interaction
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10755098	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935439	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935440	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935441	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935443	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10935446	0.86[CHB][hapmap]
rs11539489	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11706195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707427	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11710245	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11711748	0.88[CHB][hapmap]
rs11713023	0.88[CHB][hapmap]
rs11721024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11844	0.84[ASN][1000 genomes]
rs12486398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487977	0.82[ASN][1000 genomes]
rs12487983	0.84[ASN][1000 genomes]
rs12490893	0.84[ASN][1000 genomes]
rs12494971	0.88[CHB][hapmap]
rs12497443	0.88[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1560411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2115935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288634	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs2288635	0.86[ASN][1000 genomes]
rs2288636	0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2861382	0.99[ASN][1000 genomes]
rs34071952	0.82[ASN][1000 genomes]
rs36038301	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792410	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3792411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804772	0.88[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs3804773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3828398	0.85[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4683638	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683640	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683643	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683644	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683646	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683647	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4683649	0.84[ASN][1000 genomes]
rs4683651	0.80[ASN][1000 genomes]
rs55945175	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59122181	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795301	1.00[LWK][hapmap]
rs7616903	0.97[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
rs16851892	ATP1B3	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141593400-141597600	Active TSS	Fetal Kidney	kidney
2	chr3:141593400-141597600	Active TSS	HMEC	breast
3	chr3:141593400-141597600	Active TSS	NHLF	lung
4	chr3:141593400-141598000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr3:141593600-141597600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:141593600-141598400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:141593800-141597600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:141593800-141597600	Active TSS	H9 Cell Line	embryonic stem cell
9	chr3:141593800-141597600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:141593800-141597600	Active TSS	Fetal Intestine Large	intestine
11	chr3:141593800-141597600	Active TSS	HSMM	muscle
12	chr3:141593800-141598000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:141593800-141598000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:141593800-141598000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:141593800-141598400	Active TSS	H1 Cell Line	embryonic stem cell
16	chr3:141594000-141597600	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr3:141594000-141597600	Active TSS	Fetal Muscle Leg	muscle
18	chr3:141594000-141597600	Active TSS	Right Ventricle	heart
19	chr3:141594000-141598000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr3:141594200-141597600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:141594200-141598000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:141594200-141598000	Active TSS	Colonic Mucosa	Colon
23	chr3:141594400-141597600	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr3:141594400-141597600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:141594400-141597600	Active TSS	Esophagus	oesophagus
26	chr3:141594400-141597600	Active TSS	Fetal Thymus	thymus
27	chr3:141594400-141597600	Active TSS	Psoas Muscle	Psoas
28	chr3:141594400-141597600	Active TSS	NHEK	skin
29	chr3:141594400-141597800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:141594400-141597800	Active TSS	K562	blood
31	chr3:141594400-141598000	Active TSS	Hela-S3	cervix
32	chr3:141594400-141600400	Active TSS	GM12878-XiMat	blood
33	chr3:141595600-141598400	Active TSS	Right Atrium	heart
34	chr3:141596000-141598000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:141596200-141597600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:141596200-141597600	Enhancers	Stomach Mucosa	stomach
37	chr3:141596200-141597800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:141596400-141597600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:141596400-141597600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:141596400-141597600	Weak transcription	Gastric	stomach
41	chr3:141596400-141598200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr3:141596400-141609400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:141596400-141626400	Weak transcription	Pancreas	Pancrea
44	chr3:141596600-141597800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr3:141596600-141597800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr3:141596600-141597800	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr3:141596600-141597800	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr3:141596600-141597800	Flanking Active TSS	Rectal Smooth Muscle	rectum
49	chr3:141596600-141598000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:141596600-141598000	Flanking Active TSS	Duodenum Mucosa	Duodenum

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