Variant report

Variant	rs12985339
Chromosome Location	chr19:41801756-41801757
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41801299-41801905	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:41801558-41801902	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr19:41801132-41802857	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr19:41801591-41801830	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:41801576-41801763	MCF-7	breast:	n/a	n/a
6	POLR2A	chr19:41801469-41804725	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:41801570-41802019	U87	brain:	n/a	n/a
8	POLR2A	chr19:41801754-41801778	K562	blood:	n/a	n/a
9	POLR2A	chr19:41801479-41802019	U87	brain:	n/a	n/a
10	POLR2A	chr19:41801390-41806787	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41798401..41800764-chr19:41800892..41803412,2	K562	blood:
2	chr19:41795110..41797516-chr19:41801008..41803885,2	MCF-7	breast:
3	chr19:41801314..41803480-chr19:41807668..41809456,2	K562	blood:
4	chr19:41783745..41786202-chr19:41801580..41803977,3	MCF-7	breast:
5	chr19:41792573..41797879-chr19:41799335..41804103,7	K562	blood:
6	chr19:41791431..41793558-chr19:41801375..41804255,2	MCF-7	breast:
7	chr19:41799355..41806261-chr19:41812914..41817863,9	MCF-7	breast:
8	chr19:41768250..41770532-chr19:41799311..41802236,2	MCF-7	breast:
9	chr19:41776314..41777954-chr19:41800489..41802858,2	K562	blood:
10	chr19:41784680..41787150-chr19:41800943..41804189,3	K562	blood:
11	chr19:41800013..41801896-chr19:41804491..41806088,2	K562	blood:

No data

Variant related genes	Relation type
HNRNPUL1	TF binding region
ENSG00000142039	Chromatin interaction
ENSG00000239868	Chromatin interaction
ENSG00000105323	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10410836	0.98[EUR][1000 genomes]
rs10421990	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs1056854	1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11466345	0.81[JPT][hapmap]
rs11466347	0.91[ASN][1000 genomes]
rs11466359	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11879429	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11879435	0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11879562	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs11880564	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11880729	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11881940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881953	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12327659	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs12972266	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972949	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12974323	0.98[EUR][1000 genomes]
rs12974420	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12976536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12977563	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12980267	0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs12980480	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs12980942	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12981053	0.99[ASN][1000 genomes]
rs12983047	0.91[CEU][hapmap]
rs12983339	0.90[ASN][1000 genomes]
rs12984160	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12985162	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16958994	0.89[EUR][1000 genomes]
rs16958996	0.89[EUR][1000 genomes]
rs16958999	0.89[EUR][1000 genomes]
rs1865051	0.91[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs1865052	0.89[EUR][1000 genomes]
rs1865053	0.91[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs1946612	0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1946613	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2053086	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241718	0.91[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241719	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2241720	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304230	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs2304231	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2304232	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34075897	0.86[EUR][1000 genomes]
rs34322801	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34772093	0.82[ASN][1000 genomes]
rs34945449	0.89[EUR][1000 genomes]
rs35501756	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35546772	0.83[ASN][1000 genomes]
rs35812313	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3745295	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs3752705	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs3760659	0.94[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs3760660	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3816052	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs3826714	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs4456618	0.91[CEU][hapmap];0.80[CHB][hapmap];0.92[EUR][1000 genomes]
rs4591267	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61459202	0.99[ASN][1000 genomes]
rs66724427	0.98[EUR][1000 genomes]
rs67511749	0.89[EUR][1000 genomes]
rs67744888	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6957	0.91[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs7245398	0.91[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs7248164	1.00[CEU][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes]
rs7250883	0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7256416	0.98[EUR][1000 genomes]
rs7256856	0.98[EUR][1000 genomes]
rs7257310	0.91[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs7257742	0.86[EUR][1000 genomes]
rs7257825	0.98[EUR][1000 genomes]
rs7258749	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs8103839	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];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8105161	0.91[CEU][hapmap]
rs8105901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8109167	0.91[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv17637	chr19:41770228-41815282	Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12985339	FLT3LG	cis	cerebellum	SCAN
rs12985339	BAX	cis	cerebellum	SCAN
rs12985339	TSKS	cis	parietal	SCAN
rs12985339	PLEKHA4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41773000-41802400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr19:41773000-41804000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr19:41773200-41802200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:41773200-41814400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:41773400-41802200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr19:41773400-41802200	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr19:41773600-41801800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:41773600-41802200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr19:41773600-41802200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:41773600-41802200	Strong transcription	Placenta	Placenta
11	chr19:41773600-41802200	Strong transcription	HSMM	muscle
12	chr19:41773600-41802800	Weak transcription	Right Atrium	heart
13	chr19:41773600-41803400	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr19:41773600-41804400	Strong transcription	Thymus	Thymus
15	chr19:41773600-41812600	Strong transcription	A549	lung
16	chr19:41773800-41802000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr19:41773800-41802200	Strong transcription	Fetal Muscle Trunk	muscle
18	chr19:41773800-41802200	Strong transcription	Fetal Thymus	thymus
19	chr19:41773800-41802200	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr19:41773800-41802400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:41773800-41802600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr19:41773800-41802800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:41773800-41802800	Strong transcription	Fetal Stomach	stomach
24	chr19:41773800-41803200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:41773800-41803800	Strong transcription	Liver	Liver
26	chr19:41773800-41814200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:41773800-41814200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr19:41773800-41814200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:41774000-41802000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr19:41774000-41802200	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr19:41774000-41802600	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr19:41774000-41812600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:41774000-41814200	Strong transcription	Fetal Brain Female	brain
34	chr19:41774200-41801800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr19:41774200-41802200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr19:41774200-41802600	Strong transcription	Osteobl	bone
37	chr19:41774200-41803000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:41774400-41802000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr19:41774400-41802800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr19:41774400-41807600	Strong transcription	Dnd41	blood
41	chr19:41776400-41804000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr19:41780200-41815800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr19:41780600-41812000	Strong transcription	HUVEC	blood vessel
44	chr19:41782800-41808200	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr19:41783800-41814400	Strong transcription	Brain Germinal Matrix	brain
46	chr19:41788600-41815400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr19:41788800-41802000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr19:41788800-41802200	Strong transcription	Colon Smooth Muscle	Colon
49	chr19:41788800-41803000	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr19:41789000-41802200	Strong transcription	Lung	lung

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