Variant report

Variant	rs3781619
Chromosome Location	chr11:47255317-47255318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47254998..47256741-chr11:47266407..47268575,2	K562	blood:
2	chr11:47253032..47256310-chr11:47277648..47280941,3	MCF-7	breast:
3	chr11:47252711..47255857-chr11:47290010..47293384,5	MCF-7	breast:
4	chr11:47255181..47256141-chr11:47370556..47371064,2	MCF-7	breast:
5	chr11:47207072..47208935-chr11:47255110..47257481,3	MCF-7	breast:
6	chr11:47234544..47240299-chr11:47253173..47262641,20	MCF-7	breast:
7	chr11:47254776..47256305-chr11:47290925..47292746,2	K562	blood:
8	chr11:47254323..47256222-chr11:47256983..47259410,2	MCF-7	breast:
9	chr11:47253884..47256462-chr11:47268620..47272796,4	K562	blood:
10	chr11:47249459..47253221-chr11:47254419..47257374,3	K562	blood:
11	chr11:47235195..47238738-chr11:47253063..47257096,4	K562	blood:
12	chr11:47209362..47211566-chr11:47254961..47257621,2	MCF-7	breast:
13	chr11:47240491..47243810-chr11:47254933..47257331,3	MCF-7	breast:
14	chr11:47253350..47256104-chr11:47295633..47299612,4	MCF-7	breast:
15	chr11:47254425..47257069-chr11:47279237..47281162,2	MCF-7	breast:
16	chr11:47254714..47257684-chr11:47290232..47292284,2	MCF-7	breast:
17	chr11:47235195..47238586-chr11:47253063..47256921,3	K562	blood:
18	chr11:47255190..47256034-chr11:47280795..47281718,3	MCF-7	breast:
19	chr11:47240521..47243855-chr11:47254261..47256782,3	MCF-7	breast:
20	chr11:47255280..47255866-chr11:47376834..47377535,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134575	Chromatin interaction
ENSG00000256897	Chromatin interaction
ENSG00000134574	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000025434	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1051006	0.93[ASW][hapmap];0.80[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs1052373	0.82[MEX][hapmap]
rs10742797	0.81[JPT][hapmap]
rs10769253	0.80[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs10769255	0.87[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs10838663	1.00[CEU][hapmap]
rs10838664	0.82[CHD][hapmap]
rs10838681	0.80[CHD][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.80[YRI][hapmap]
rs10838687	0.88[ASW][hapmap];0.95[MEX][hapmap];0.83[YRI][hapmap]
rs10838689	0.81[ASW][hapmap];0.80[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs10838692	0.82[MEX][hapmap]
rs11039144	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039148	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11039155	0.85[EUR][1000 genomes]
rs12574081	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12574410	1.00[CEU][hapmap]
rs1449626	0.82[AMR][1000 genomes]
rs1449627	0.82[MEX][hapmap]
rs16938581	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2242261	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2242262	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279238	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2290146	0.94[ASW][hapmap];0.80[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap]
rs2290148	0.94[ASW][hapmap];0.80[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.86[YRI][hapmap]
rs2305280	0.88[ASW][hapmap]
rs2306353	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2596397	0.87[AMR][1000 genomes]
rs2596398	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2633080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2633083	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957873	0.94[ASW][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.82[MEX][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs326224	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3729802	0.85[CEU][hapmap];0.85[YRI][hapmap]
rs3758670	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3781620	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3824866	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4647725	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4647726	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4647737	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4647741	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4647754	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4647757	0.93[AMR][1000 genomes]
rs4752965	1.00[CEU][hapmap]
rs4752972	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4752973	0.94[ASW][hapmap];0.81[CHB][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs4752977	0.94[ASW][hapmap];0.80[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.90[YRI][hapmap]
rs4752983	1.00[ASW][hapmap];0.80[CEU][hapmap];0.90[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap]
rs59567949	0.82[AMR][1000 genomes]
rs7118396	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7120118	0.82[MEX][hapmap]
rs7120158	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7124958	0.85[YRI][hapmap]
rs7130006	0.82[CHD][hapmap]
rs7395496	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs753992	0.80[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs7933246	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7937410	0.82[CHD][hapmap]
rs7940240	0.82[CHD][hapmap]
rs7947269	0.82[AMR][1000 genomes]
rs830083	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs830084	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs830085	0.82[MEX][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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3781619	ACP2	cis	multi-tissue	Pritchard
rs3781619	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs3781619	ACP2	cis	Thyroid	GTEx
rs3781619	NR1H3	cis	multi-tissue	Pritchard
rs3781619	DDB2	Cis_1M	lymphoblastoid	RTeQTL
rs3781619	MADD	cis	lymphoblastoid	seeQTL
rs3781619	ACP2	cis	lymphoblastoid	seeQTL
rs3781619	DDB2	cis	lymphoblastoid	seeQTL
rs3781619	PTPMT1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47238400-47255800	Weak transcription	Brain Anterior Caudate	brain
2	chr11:47238400-47269400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:47238600-47255400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:47238600-47255400	Weak transcription	Right Ventricle	heart
5	chr11:47238600-47255600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr11:47238600-47255800	Weak transcription	Brain Substantia Nigra	brain
7	chr11:47238600-47255800	Weak transcription	Right Atrium	heart
8	chr11:47238600-47256000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr11:47238600-47259600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr11:47238600-47261000	Weak transcription	Small Intestine	intestine
11	chr11:47239800-47255600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr11:47239800-47255600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr11:47240000-47260200	Weak transcription	Fetal Brain Female	brain
14	chr11:47240200-47255400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr11:47240200-47255600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr11:47240200-47255800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr11:47240200-47256000	Weak transcription	Gastric	stomach
18	chr11:47240200-47266600	Weak transcription	Fetal Brain Male	brain
19	chr11:47240400-47255800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr11:47241400-47255600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr11:47241800-47256000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:47242000-47255800	Weak transcription	Left Ventricle	heart
23	chr11:47242200-47255400	Weak transcription	Brain Hippocampus Middle	brain
24	chr11:47242200-47258200	Weak transcription	Fetal Lung	lung
25	chr11:47242400-47256000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr11:47242400-47257800	Weak transcription	K562	blood
27	chr11:47242400-47258000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:47242400-47258000	Weak transcription	Primary B cells from cord blood	blood
29	chr11:47242400-47269200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:47242600-47259600	Weak transcription	Brain Germinal Matrix	brain
31	chr11:47242600-47260200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr11:47243000-47255600	Weak transcription	Fetal Heart	heart
33	chr11:47243600-47269200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr11:47244400-47255400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr11:47245400-47255400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:47246200-47255400	Weak transcription	HSMM	muscle
37	chr11:47246200-47256600	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr11:47246400-47256800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:47246600-47267800	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr11:47246800-47256200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr11:47247400-47267600	Strong transcription	Thymus	Thymus
42	chr11:47247800-47256000	Weak transcription	Hela-S3	cervix
43	chr11:47247800-47256600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr11:47248200-47255800	Weak transcription	Colonic Mucosa	Colon
45	chr11:47248200-47258600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr11:47248200-47259400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr11:47248200-47265200	Strong transcription	GM12878-XiMat	blood
48	chr11:47248600-47255600	Weak transcription	Adipose Nuclei	Adipose
49	chr11:47248600-47260800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr11:47249400-47259400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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