Variant report

Variant	rs17046567
Chromosome Location	chr2:55219516-55219517
allele	G/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	chr2:55219099-55219735	U87	brain:	n/a	n/a
2	POLR2A	chr2:55219175-55219527	SK-N-SH	brain:	n/a	n/a
3	FOS	chr2:55219382-55219713	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr2:55219240-55219546	U87	brain:	n/a	n/a
5	POLR2A	chr2:55219003-55219592	SK-N-SH	brain:	n/a	n/a
6	FOS	chr2:55219395-55219708	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr2:55219099-55219729	U87	brain:	n/a	n/a
8	POLR2A	chr2:55218867-55219546	U87	brain:	n/a	n/a
9	FOS	chr2:55219386-55219723	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr2:55219384-55219707	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr2:55218294-55219846	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55216168..55220754-chr2:55221880..55224884,4	MCF-7	breast:
2	chr2:55219389..55222736-chr2:55233484..55237490,3	MCF-7	breast:

Variant related genes	Relation type
RTN4	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10084445	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10170102	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10173203	0.96[YRI][hapmap]
rs10175952	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10179491	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10180207	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10181115	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10182203	0.85[EUR][1000 genomes]
rs10191684	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs10191748	0.85[AMR][1000 genomes]
rs10197533	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10198096	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10207701	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11125554	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13385999	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13387710	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13394823	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs13394824	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs13400353	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13401780	0.81[EUR][1000 genomes]
rs13401937	0.84[AFR][1000 genomes]
rs13416852	0.81[EUR][1000 genomes]
rs17046569	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3198123	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs34928331	0.89[AFR][1000 genomes]
rs3806572	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4358163	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs60989108	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545470	0.81[EUR][1000 genomes]
rs6715980	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6725187	0.96[AMR][1000 genomes]
rs6744637	0.81[EUR][1000 genomes]
rs72912579	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7570298	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7584992	0.96[AMR][1000 genomes]
rs7592869	0.81[EUR][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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
3	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:55203800-55222600	Weak transcription	Spleen	Spleen
5	chr2:55203800-55223800	Weak transcription	Pancreas	Pancrea
6	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
7	chr2:55205200-55220600	Weak transcription	Small Intestine	intestine
8	chr2:55205200-55223800	Weak transcription	Left Ventricle	heart
9	chr2:55210000-55228200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:55211200-55232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:55212200-55220600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:55212600-55220200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:55212600-55226400	Weak transcription	Fetal Stomach	stomach
14	chr2:55213800-55226400	Weak transcription	Ovary	ovary
15	chr2:55214200-55224600	Weak transcription	Primary T cells from cord blood	blood
16	chr2:55214200-55225000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:55214200-55234400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:55214400-55222800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:55214400-55232800	Weak transcription	Fetal Brain Female	brain
20	chr2:55214600-55225600	Weak transcription	NH-A	brain
21	chr2:55214600-55226000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:55214800-55220600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:55214800-55221600	Weak transcription	HSMMtube	muscle
24	chr2:55214800-55221800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:55214800-55222000	Weak transcription	GM12878-XiMat	blood
26	chr2:55214800-55223600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:55214800-55223800	Weak transcription	Gastric	stomach
28	chr2:55214800-55224400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:55214800-55224400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:55214800-55224600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:55214800-55225000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr2:55214800-55225000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:55214800-55225200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr2:55214800-55225200	Weak transcription	Fetal Brain Male	brain
35	chr2:55214800-55225600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:55214800-55225600	Weak transcription	Brain Germinal Matrix	brain
37	chr2:55214800-55226000	Weak transcription	HUVEC	blood vessel
38	chr2:55214800-55226400	Weak transcription	Fetal Muscle Leg	muscle
39	chr2:55214800-55226400	Weak transcription	Fetal Thymus	thymus
40	chr2:55214800-55227200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:55214800-55227200	Weak transcription	HepG2	liver
42	chr2:55214800-55228800	Weak transcription	Fetal Intestine Large	intestine
43	chr2:55214800-55230600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr2:55214800-55231600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:55214800-55234200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:55214800-55236800	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr2:55215000-55222600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:55215000-55225200	Weak transcription	Liver	Liver
49	chr2:55215000-55225800	Weak transcription	Primary B cells from cord blood	blood
50	chr2:55215000-55225800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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