Variant report

Variant	rs10409265
Chromosome Location	chr19:19115002-19115003
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	chr19:19114056-19115416	K562	blood:	n/a	n/a
2	POLR2A	chr19:19114390-19115080	K562	blood:	n/a	n/a
3	POLR2A	chr19:19114475-19115373	HL-60	blood:	n/a	n/a
4	POLR2A	chr19:19114909-19115065	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:19114042-19115416	K562	blood:	n/a	n/a
6	POLR2A	chr19:19114337-19115185	K562	blood:	n/a	n/a
7	POLR2A	chr19:19114953-19115107	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19111292..19114373-chr19:19114912..19119254,5	K562	blood:

Variant related genes	Relation type
SUGP2	TF binding region
ENSG00000064607	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10402411	0.85[AFR][1000 genomes]
rs10404020	0.92[YRI][hapmap];0.95[AFR][1000 genomes]
rs10404879	1.00[ASW][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs10406282	1.00[ASW][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs10406341	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs10406496	0.81[AFR][1000 genomes]
rs10407260	1.00[ASW][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs10407753	0.81[AFR][1000 genomes]
rs10408567	0.81[AFR][1000 genomes]
rs10409297	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10409395	1.00[ASW][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs10411413	0.92[YRI][hapmap]
rs10412101	0.88[AFR][1000 genomes]
rs10413216	1.00[MEX][hapmap];0.92[YRI][hapmap]
rs10414535	1.00[ASW][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs10414859	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10415998	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10416041	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs10416054	1.00[ASW][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs10416240	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs10416250	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs10416730	0.88[AFR][1000 genomes]
rs10417310	0.88[AFR][1000 genomes]
rs10417682	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs10417995	0.84[AFR][1000 genomes]
rs10418688	0.88[AFR][1000 genomes]
rs10419114	0.88[AFR][1000 genomes]
rs10419307	0.88[AFR][1000 genomes]
rs10420479	1.00[ASW][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs10420559	0.82[ASW][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs10422058	1.00[MEX][hapmap];0.85[YRI][hapmap]
rs10422238	0.86[AFR][1000 genomes]
rs10423129	0.88[AFR][1000 genomes]
rs10423504	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10426131	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs13344835	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs13345246	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs28369262	0.81[AFR][1000 genomes]
rs28376498	0.83[AFR][1000 genomes]
rs28416794	0.90[AFR][1000 genomes]
rs28421315	0.88[AFR][1000 genomes]
rs28445835	1.00[ASW][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs28475392	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28477157	0.88[AFR][1000 genomes]
rs28477961	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28507927	0.88[AFR][1000 genomes]
rs28530647	0.85[AFR][1000 genomes]
rs28533991	0.97[AFR][1000 genomes]
rs28619464	0.83[AFR][1000 genomes]
rs28628081	0.88[AFR][1000 genomes]
rs28699197	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28720008	0.88[AFR][1000 genomes]
rs2872205	1.00[MEX][hapmap]
rs35646935	0.88[AFR][1000 genomes]
rs6511012	0.82[ASW][hapmap];1.00[MEX][hapmap];0.92[YRI][hapmap]
rs7248183	1.00[MEX][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs7252172	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8106189	0.85[YRI][hapmap];0.88[AFR][1000 genomes]

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	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv2435	chr19:19077432-19122579	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19100200-19117400	Strong transcription	Fetal Intestine Small	intestine
2	chr19:19100600-19122800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:19101000-19125600	Strong transcription	Thymus	Thymus
4	chr19:19101000-19133000	Strong transcription	Fetal Thymus	thymus
5	chr19:19101200-19126000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:19101200-19130400	Strong transcription	Duodenum Mucosa	Duodenum
7	chr19:19101200-19140200	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr19:19101400-19130400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr19:19101400-19142000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr19:19101600-19130400	Strong transcription	Primary T cells from cord blood	blood
11	chr19:19101600-19130400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:19102000-19130200	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr19:19102000-19132000	Strong transcription	Dnd41	blood
14	chr19:19102600-19122600	Weak transcription	Fetal Heart	heart
15	chr19:19103200-19130200	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr19:19103600-19123600	Strong transcription	HepG2	liver
17	chr19:19106800-19119200	Weak transcription	Stomach Mucosa	stomach
18	chr19:19106800-19143000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr19:19107000-19119000	Weak transcription	Fetal Kidney	kidney
20	chr19:19107200-19130200	Strong transcription	Brain Germinal Matrix	brain
21	chr19:19107200-19142600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:19107400-19125800	Strong transcription	Fetal Muscle Leg	muscle
23	chr19:19107600-19127200	Strong transcription	Fetal Intestine Large	intestine
24	chr19:19107600-19130200	Strong transcription	Brain Hippocampus Middle	brain
25	chr19:19107600-19142600	Strong transcription	Fetal Stomach	stomach
26	chr19:19107800-19130200	Strong transcription	Placenta	Placenta
27	chr19:19107800-19130400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:19107800-19130400	Strong transcription	Fetal Brain Female	brain
29	chr19:19108000-19142000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:19108000-19142800	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr19:19108200-19116400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:19108200-19130400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:19108200-19142600	Weak transcription	Right Atrium	heart
34	chr19:19108600-19119600	Strong transcription	NHDF-Ad	bronchial
35	chr19:19108600-19130600	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr19:19108600-19142200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:19108600-19142800	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr19:19108800-19116200	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr19:19108800-19116200	Strong transcription	Rectal Smooth Muscle	rectum
40	chr19:19108800-19123800	Strong transcription	NHEK	skin
41	chr19:19108800-19127400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:19108800-19130400	Strong transcription	Primary B cells from peripheral blood	blood
43	chr19:19109000-19130400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:19109000-19141800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr19:19109200-19121800	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr19:19109400-19130200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr19:19109400-19130200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr19:19109400-19142400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr19:19109800-19130200	Strong transcription	GM12878-XiMat	blood
50	chr19:19110200-19130400	Strong transcription	Stomach Smooth Muscle	stomach

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