Variant report

Variant	rs2061333
Chromosome Location	chr19:44614208-44614209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:44613651-44614694	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44611565..44614380-chr19:44615671..44618988,4	MCF-7	breast:

Variant related genes	Relation type
ZNF225	TF binding region
ENSG00000256294	Chromatin interaction
ENSG00000186019	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10406335	0.91[CHB][hapmap];0.90[CHD][hapmap]
rs10408901	0.91[CHB][hapmap]
rs10410306	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10413195	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs10420143	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10853771	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1236715	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs1236716	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs2061332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284978	0.87[CHB][hapmap]
rs2284980	0.91[CHB][hapmap]
rs2284981	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[EUR][1000 genomes]
rs28446946	0.92[ASN][1000 genomes]
rs28539456	0.92[ASN][1000 genomes]
rs3172	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3200505	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3746319	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3746321	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4239529	0.91[CHB][hapmap]
rs4429390	0.91[CHB][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs4459653	0.91[CHB][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap]
rs4508518	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802204	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4802205	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802206	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4802207	0.88[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4802208	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4803676	0.91[CHB][hapmap]
rs4803678	0.87[CHB][hapmap]
rs4803680	0.86[CHB][hapmap]
rs4803681	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55876899	0.86[ASN][1000 genomes]
rs56353321	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62115524	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62115526	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6509142	0.82[LWK][hapmap]
rs7250004	0.93[ASN][1000 genomes]
rs7250005	0.91[ASN][1000 genomes]
rs7253485	0.86[EUR][1000 genomes]
rs7508149	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8099869	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8104573	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8105860	0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8108021	0.88[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8108404	0.90[ASN][1000 genomes]
rs8113750	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9304638	0.91[CHB][hapmap]

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	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Alzheimer's disease	19118814	GWAS catalog

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2061333	SNRPD2	cis	cerebellum	SCAN
rs2061333	FUT2	cis	parietal	SCAN
rs2061333	CLPTM1	cis	cerebellum	SCAN
rs2061333	KLK10	cis	cerebellum	SCAN
rs2061333	APOE	cis	parietal	SCAN
rs2061333	CPT1C	cis	cerebellum	SCAN
rs2061333	ZNF221	cis	Lymphoblastoid	GTEx
rs2061333	ZNF224	Cis_1M	lymphoblastoid	RTeQTL
rs2061333	ZNF221	cis	multi-tissue	Pritchard
rs2061333	SNORD34	cis	parietal	SCAN
rs2061333	SIGLEC12	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44600400-44616200	ZNF genes & repeats	Liver	Liver
2	chr19:44600800-44614600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:44604800-44616000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:44605200-44614600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:44606600-44616400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr19:44608200-44614600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:44608200-44615800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:44608400-44614400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:44608400-44614600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
10	chr19:44608400-44616000	ZNF genes & repeats	Fetal Brain Female	brain
11	chr19:44608600-44615800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
12	chr19:44610200-44614600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
13	chr19:44610400-44614600	ZNF genes & repeats	Fetal Brain Male	brain
14	chr19:44612000-44616200	Weak transcription	HepG2	liver
15	chr19:44612200-44616000	Weak transcription	Fetal Thymus	thymus
16	chr19:44612400-44614800	Weak transcription	Fetal Intestine Large	intestine
17	chr19:44612400-44615200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:44612400-44616000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr19:44612400-44616000	Weak transcription	Pancreas	Pancrea
20	chr19:44612400-44616200	Weak transcription	Gastric	stomach
21	chr19:44612400-44616400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr19:44612600-44614400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:44612600-44615600	Weak transcription	HSMMtube	muscle
24	chr19:44612600-44615800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr19:44612600-44616000	Weak transcription	Placenta	Placenta
26	chr19:44612800-44614400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:44612800-44615400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr19:44612800-44615600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:44612800-44615600	Weak transcription	NHDF-Ad	bronchial
30	chr19:44612800-44615800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:44612800-44615800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:44612800-44615800	Weak transcription	NHEK	skin
33	chr19:44612800-44615800	Weak transcription	Osteobl	bone
34	chr19:44612800-44616000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:44612800-44616000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr19:44612800-44616200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:44612800-44616200	Weak transcription	Ovary	ovary
38	chr19:44612800-44616200	Weak transcription	Thymus	Thymus
39	chr19:44612800-44617000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:44613000-44614400	Weak transcription	Brain Germinal Matrix	brain
41	chr19:44613000-44614800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:44613000-44615200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr19:44613000-44615800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr19:44613000-44616000	Weak transcription	Brain Angular Gyrus	brain
45	chr19:44613000-44616000	Weak transcription	Fetal Kidney	kidney
46	chr19:44613200-44614600	Weak transcription	Left Ventricle	heart
47	chr19:44613200-44615600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:44613200-44615800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr19:44613600-44614600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:44613600-44614800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

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