Variant report

Variant	rs10933409
Chromosome Location	chr2:233629386-233629387
allele	A/G
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	chr2:233629344-233629505	K562	blood:	n/a	n/a
2	POLR2A	chr2:233629318-233629553	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233627414..233629760-chr2:233639796..233641450,2	MCF-7	breast:

Variant related genes	Relation type
GIGYF2	TF binding region
ENSG00000115474	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs1022330	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1044480	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933411	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10933412	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11555646	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676216	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11679079	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11687128	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690474	0.86[EUR][1000 genomes]
rs11692545	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12472839	0.94[EUR][1000 genomes]
rs12474040	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478564	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694917	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12987513	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990821	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12991088	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12997185	0.90[EUR][1000 genomes]
rs13003675	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13003738	0.81[ASN][1000 genomes]
rs13004406	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13007783	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13008942	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011298	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13013142	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13021246	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024793	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13035829	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13424351	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1446308	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446310	0.91[ASN][1000 genomes]
rs1446311	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1801251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867778	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1947105	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2012221	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2044449	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2100053	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2305137	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2305141	0.91[ASN][1000 genomes]
rs2592102	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2592105	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2592113	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2674839	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2675971	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2675973	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2675974	0.83[EUR][1000 genomes]
rs283466	0.91[ASN][1000 genomes]
rs283468	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs283469	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs283471	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs283474	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs283475	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs283476	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs283477	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs283478	0.82[ASN][1000 genomes]
rs283479	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283480	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283481	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283484	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283485	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283486	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33980184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34880628	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35085837	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35212961	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35285732	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35362030	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35395584	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35621474	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36007169	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816334	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3817311	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4452130	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4458205	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4517962	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4973053	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4973054	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4973056	0.82[EUR][1000 genomes]
rs4973559	0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4973560	0.88[ASN][1000 genomes]
rs4973561	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs56777991	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437074	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66549961	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67013068	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714245	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717841	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719061	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6724117	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6732136	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6733151	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738386	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6739638	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6745879	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746294	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6747645	0.96[EUR][1000 genomes]
rs6748027	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761324	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71421663	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs737028	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7558609	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7562712	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7573208	0.89[ASN][1000 genomes]
rs7578299	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7587309	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7589201	0.83[EUR][1000 genomes]
rs7591176	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7592717	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7606090	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs778166	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs895430	0.83[EUR][1000 genomes]
rs9653383	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9679089	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs983430	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs991873	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:233585200-233655000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:233587000-233630600	Weak transcription	Psoas Muscle	Psoas
4	chr2:233602400-233633200	Weak transcription	Aorta	Aorta
5	chr2:233606200-233638400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:233606800-233633200	Weak transcription	Stomach Mucosa	stomach
7	chr2:233606800-233636800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:233609200-233630800	Strong transcription	HepG2	liver
9	chr2:233611600-233645600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr2:233612000-233631000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:233612000-233634000	Strong transcription	Primary B cells from peripheral blood	blood
12	chr2:233612000-233634000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:233612000-233640000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:233612000-233644600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr2:233612200-233633800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:233612200-233634000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:233612200-233634400	Strong transcription	Fetal Thymus	thymus
18	chr2:233612200-233638400	Strong transcription	Placenta	Placenta
19	chr2:233612600-233637200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:233613800-233635600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:233614000-233636800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:233614400-233632800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:233614600-233643600	Weak transcription	Small Intestine	intestine
24	chr2:233617000-233636600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr2:233618600-233635600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:233620200-233640000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:233621400-233632400	Weak transcription	K562	blood
28	chr2:233621400-233644400	Strong transcription	Liver	Liver
29	chr2:233622400-233635600	Weak transcription	Esophagus	oesophagus
30	chr2:233623000-233632600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:233623400-233630800	Strong transcription	Left Ventricle	heart
32	chr2:233623400-233631400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:233623400-233632400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr2:233623400-233633800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:233623600-233636800	Strong transcription	Fetal Intestine Large	intestine
36	chr2:233623800-233631400	Strong transcription	Dnd41	blood
37	chr2:233623800-233634200	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:233624200-233629800	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr2:233624400-233629400	Strong transcription	GM12878-XiMat	blood
40	chr2:233624400-233630400	Strong transcription	HSMM	muscle
41	chr2:233624400-233630800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:233624400-233634000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr2:233624400-233640000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:233624600-233630800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:233624800-233631000	Strong transcription	Osteobl	bone
46	chr2:233624800-233634000	Strong transcription	Adipose Nuclei	Adipose
47	chr2:233624800-233640000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:233625000-233629400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:233625000-233629400	Strong transcription	Fetal Muscle Leg	muscle
50	chr2:233625000-233629600	Strong transcription	NH-A	brain

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