Variant report

Variant	rs3747965
Chromosome Location	chr1:94342564-94342565
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:94341699-94343563	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:94336837..94340766-chr1:94341847..94346212,6	K562	blood:
2	chr1:94332079..94335914-chr1:94341026..94344306,4	K562	blood:
3	chr1:94311992..94315197-chr1:94341852..94346150,3	MCF-7	breast:
4	chr1:94340857..94342610-chr1:94343304..94345726,2	K562	blood:
5	chr1:94340990..94343514-chr1:94369991..94373741,3	K562	blood:
6	chr1:94342014..94348814-chr1:94369991..94376733,14	K562	blood:
7	chr1:94340793..94342610-chr1:94344226..94345915,2	K562	blood:
8	chr1:94340612..94342966-chr1:94406740..94409371,2	K562	blood:
9	chr1:94341311..94342954-chr1:94373735..94375805,2	MCF-7	breast:
10	chr1:94310214..94315053-chr1:94342432..94346579,12	K562	blood:

No data

Variant related genes	Relation type
DNTTIP2	TF binding region
ENSG00000211575	Chromatin interaction
ENSG00000067334	Chromatin interaction
ENSG00000023909	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10489602	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10489603	0.93[GIH][hapmap];0.82[EUR][1000 genomes]
rs10489604	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10782966	0.85[EUR][1000 genomes]
rs10782967	0.85[EUR][1000 genomes]
rs11165020	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11165022	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs11165024	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11165026	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs12027630	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12041975	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs12122113	0.87[EUR][1000 genomes]
rs12134359	1.00[CEU][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs12137687	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12140446	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12143274	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12143279	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12563731	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12565614	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12565817	0.89[GIH][hapmap]
rs12566531	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12734571	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12739186	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12745990	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12752298	0.88[EUR][1000 genomes]
rs1398798	0.96[CEU][hapmap];0.91[JPT][hapmap]
rs1884018	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1980083	0.81[CEU][hapmap]
rs2143990	0.86[EUR][1000 genomes]
rs2143992	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs2235971	0.86[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];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2273166	0.89[CHB][hapmap]
rs2391315	0.82[JPT][hapmap]
rs2391322	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2747039	0.85[EUR][1000 genomes]
rs2747041	0.85[EUR][1000 genomes]
rs2747043	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2747045	0.96[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2747050	0.84[EUR][1000 genomes]
rs2818160	0.85[EUR][1000 genomes]
rs2818162	0.85[EUR][1000 genomes]
rs2818164	0.86[EUR][1000 genomes]
rs2818169	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3000471	0.86[EUR][1000 genomes]
rs4075523	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4141736	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4141737	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];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4240955	0.85[EUR][1000 genomes]
rs4240956	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4314890	0.85[EUR][1000 genomes]
rs4350209	0.86[ASW][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs4847253	0.81[EUR][1000 genomes]
rs4847256	0.85[CEU][hapmap]
rs4847264	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs4847265	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6664719	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];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6681265	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs6685747	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7364910	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8179391	0.85[EUR][1000 genomes]
rs871854	0.81[EUR][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3747965	RP11-488P3.1	cis	Thyroid	GTEx
rs3747965	RP11-488P3.1	cis	Artery Tibial	GTEx
rs3747965	RP11-488P3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs3747965	RP11-488P3.1	cis	Nerve Tibial	GTEx
rs3747965	RP11-488P3.1	cis	Esophagus Muscularis	GTEx
rs3747965	RP11-488P3.1	cis	lung	GTEx
rs3747965	RP11-488P3.1	cis	Heart Left Ventricle	GTEx
rs3747965	RP11-488P3.1	cis	Adipose Subcutaneous	GTEx
rs3747965	RP11-488P3.1	cis	Muscle Skeletal	GTEx
rs3747965	RP11-488P3.1	cis	Stomach	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94322200-94343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:94329800-94343600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:94330600-94343600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:94332800-94343200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:94332800-94343200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:94333200-94343200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:94333800-94343000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:94334000-94343000	Strong transcription	Fetal Thymus	thymus
9	chr1:94334000-94343400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:94334200-94343200	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr1:94334200-94343200	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr1:94334200-94343200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:94334200-94343200	Strong transcription	Fetal Muscle Leg	muscle
14	chr1:94334200-94343400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:94334200-94343400	Strong transcription	Placenta	Placenta
16	chr1:94334400-94343200	Strong transcription	NH-A	brain
17	chr1:94334400-94343400	Weak transcription	Fetal Heart	heart
18	chr1:94334600-94342800	Strong transcription	Brain Hippocampus Middle	brain
19	chr1:94334600-94342800	Strong transcription	HSMM	muscle
20	chr1:94334600-94343000	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr1:94334600-94343200	Strong transcription	Fetal Intestine Large	intestine
22	chr1:94334600-94343200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr1:94334600-94343400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr1:94338400-94343800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:94340000-94343200	Strong transcription	HSMMtube	muscle
26	chr1:94340400-94343200	Weak transcription	Stomach Mucosa	stomach
27	chr1:94340400-94343800	Weak transcription	Aorta	Aorta
28	chr1:94340400-94344000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:94340600-94343200	Weak transcription	Gastric	stomach
30	chr1:94340600-94343200	Weak transcription	Pancreas	Pancrea
31	chr1:94340600-94343200	Weak transcription	Spleen	Spleen
32	chr1:94340600-94343600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:94340600-94343600	Weak transcription	Lung	lung
34	chr1:94340600-94344000	Weak transcription	Esophagus	oesophagus
35	chr1:94340600-94344000	Weak transcription	Ovary	ovary
36	chr1:94340800-94342800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:94341000-94343400	Weak transcription	Fetal Stomach	stomach
38	chr1:94341000-94343400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:94341200-94343400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:94341200-94343400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
41	chr1:94341600-94342600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:94341600-94342600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:94341600-94343000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
44	chr1:94341600-94343000	Genic enhancers	HepG2	liver
45	chr1:94341600-94343200	Genic enhancers	Primary monocytes fromperipheralblood	blood
46	chr1:94341600-94343200	Genic enhancers	Primary B cells from peripheral blood	blood
47	chr1:94341600-94343200	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr1:94341600-94343400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:94341600-94343400	Genic enhancers	Primary B cells from cord blood	blood
50	chr1:94341600-94343400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood

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