Variant report

Variant	rs1704925
Chromosome Location	chr12:104928750-104928751
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104919574..104922787-chr12:104926132..104929881,3	MCF-7	breast:
2	chr12:104928335..104930569-chr12:104932517..104934714,3	K562	blood:
3	chr12:104928335..104930569-chr12:104932638..104934714,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11613208	0.92[CEU][hapmap]
rs1553836	0.96[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs1553839	0.92[EUR][1000 genomes]
rs1625417	0.93[EUR][1000 genomes]
rs1626422	0.92[EUR][1000 genomes]
rs1628116	0.96[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs1704903	1.00[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs1704905	0.95[EUR][1000 genomes]
rs1704915	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704916	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1704917	0.96[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs1704918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704921	1.00[CEU][hapmap];0.92[GIH][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs1704922	1.00[CEU][hapmap];0.92[GIH][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs1704923	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs1704924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704929	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17812021	0.83[ASN][1000 genomes]
rs1795851	0.88[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1795852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795853	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795855	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795856	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1795861	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1795862	0.96[CEU][hapmap];0.97[GIH][hapmap];0.81[LWK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1795864	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1795867	0.96[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1795868	0.92[EUR][1000 genomes]
rs1795870	0.96[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1795872	0.96[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs1973589	0.96[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2055861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2665748	1.00[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs2706273	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6539159	0.92[CEU][hapmap]
rs7968613	0.92[CEU][hapmap]
rs907097	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][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	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1704925	GOLGA2B	cis	parietal	SCAN
rs1704925	UTP20	cis	cerebellum	SCAN
rs1704925	KIAA1033	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104915600-104936600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:104918000-104934200	Weak transcription	A549	lung
3	chr12:104919200-104935000	Weak transcription	Primary T cells from cord blood	blood
4	chr12:104920600-104929400	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:104921000-104929200	Weak transcription	Right Ventricle	heart
6	chr12:104921400-104931600	Weak transcription	Gastric	stomach
7	chr12:104921400-104939000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:104923200-104930200	Weak transcription	NHEK	skin
9	chr12:104923400-104929800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:104923400-104930000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:104924000-104930600	Weak transcription	Placenta	Placenta
12	chr12:104924800-104939600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:104925400-104930600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr12:104925400-104931000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr12:104925600-104929200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:104925600-104931400	Enhancers	Primary B cells from peripheral blood	blood
17	chr12:104925800-104929000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:104926000-104930200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr12:104926000-104931000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:104926600-104929200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr12:104926600-104930400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr12:104926800-104929200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:104927200-104930200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:104927200-104930200	Weak transcription	Thymus	Thymus
25	chr12:104927200-104930200	Weak transcription	HMEC	breast
26	chr12:104927200-104943000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr12:104927400-104929000	Enhancers	Primary B cells from cord blood	blood
28	chr12:104927400-104929200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr12:104927400-104929200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:104927400-104929200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr12:104927400-104930200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:104927600-104929000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:104927600-104929400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:104927600-104929400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:104927600-104929600	Enhancers	Brain Germinal Matrix	brain
36	chr12:104927800-104929000	Weak transcription	Dnd41	blood
37	chr12:104927800-104929400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:104927800-104929400	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr12:104927800-104929400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr12:104928000-104929200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:104928000-104929200	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr12:104928000-104929200	Enhancers	Spleen	Spleen
43	chr12:104928000-104929400	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr12:104928000-104929400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:104928000-104929600	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr12:104928000-104929600	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr12:104928000-104929600	Enhancers	Fetal Brain Male	brain
48	chr12:104928200-104928800	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr12:104928200-104929000	Enhancers	Fetal Kidney	kidney
50	chr12:104928200-104929200	Enhancers	NH-A	brain

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