Variant report

Variant	rs2193270
Chromosome Location	chr12:12561484-12561485
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12548191..12550928-chr12:12559817..12561583,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1019340	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1019341	0.81[ASN][1000 genomes]
rs1030069	0.89[JPT][hapmap]
rs10459098	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10505765	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs10743982	0.89[JPT][hapmap]
rs10743985	0.82[ASN][1000 genomes]
rs10772563	0.82[ASN][1000 genomes]
rs10845533	0.82[ASN][1000 genomes]
rs10845539	0.82[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10845541	0.82[ASN][1000 genomes]
rs10845545	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10845546	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs11561172	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs11609375	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs11829916	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11834080	0.80[MEX][hapmap]
rs1468876	0.81[ASN][1000 genomes]
rs16907990	0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs16908006	0.85[ASW][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs16908019	0.96[AFR][1000 genomes]
rs16908050	0.84[ASN][1000 genomes]
rs16908059	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs16908062	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs16908072	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs16908076	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs16908101	0.94[CHB][hapmap];0.93[CHD][hapmap];0.80[ASN][1000 genomes]
rs1861674	0.93[ASW][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs2193269	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216264	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2417187	0.86[ASN][1000 genomes]
rs28853875	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751262	0.81[CHB][hapmap]
rs3803098	0.81[CHB][hapmap]
rs3925170	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs4488294	0.82[ASN][1000 genomes]
rs4547192	0.82[ASN][1000 genomes]
rs4763824	0.94[AFR][1000 genomes]
rs4763825	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs4763826	0.82[ASN][1000 genomes]
rs4763827	0.84[AFR][1000 genomes]
rs4763828	0.87[AFR][1000 genomes]
rs4763829	0.89[JPT][hapmap]
rs4763830	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs56089442	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56701819	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56796062	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56915387	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57348917	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58218344	0.90[AFR][1000 genomes]
rs60253266	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61543155	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6488520	0.81[CEU][hapmap]
rs6488521	0.81[AFR][1000 genomes]
rs6488523	0.93[YRI][hapmap];0.87[AFR][1000 genomes]
rs6488524	0.87[AFR][1000 genomes]
rs6488526	0.82[ASN][1000 genomes]
rs6488527	1.00[ASW][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs7134787	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs7135655	0.82[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs714480	0.95[AFR][1000 genomes]
rs7295080	0.81[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs7300150	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7306292	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs7309503	0.81[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs7309982	0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7310012	0.84[JPT][hapmap]
rs7311364	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs7313825	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs7315626	0.81[ASN][1000 genomes]
rs73283441	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7486371	0.87[CHB][hapmap]
rs7953025	0.82[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs7954752	0.82[ASN][1000 genomes]
rs7967038	0.81[ASN][1000 genomes]
rs7967111	0.84[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7967230	0.84[JPT][hapmap]
rs7967466	0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7969020	0.81[ASN][1000 genomes]
rs7969252	0.82[ASN][1000 genomes]
rs7969270	0.81[ASN][1000 genomes]
rs7969849	0.82[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7969984	0.82[ASN][1000 genomes]
rs7975061	0.96[YRI][hapmap]
rs7978842	0.88[AFR][1000 genomes]
rs7980390	0.93[ASW][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap]
rs879445	0.81[ASN][1000 genomes]
rs888198	0.80[YRI][hapmap]
rs888200	0.82[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs9738409	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2193270	CLEC4E	cis	parietal	SCAN
rs2193270	LOH12CR1	cis	parietal	SCAN
rs2193270	GPRC5D	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12537200-12576000	Weak transcription	Primary B cells from cord blood	blood
2	chr12:12538600-12561800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:12541400-12562800	Weak transcription	Psoas Muscle	Psoas
4	chr12:12552000-12569000	Weak transcription	Hela-S3	cervix
5	chr12:12556600-12561600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr12:12556800-12561800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:12557000-12561600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:12557200-12572400	Weak transcription	Primary T cells from cord blood	blood
9	chr12:12557800-12565000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:12558000-12586000	Weak transcription	Pancreas	Pancrea
11	chr12:12559200-12564800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr12:12559400-12564800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:12560200-12562200	Weak transcription	Fetal Intestine Small	intestine
14	chr12:12560200-12564800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:12560200-12564800	Weak transcription	HepG2	liver
16	chr12:12560800-12561600	Enhancers	Brain Hippocampus Middle	brain
17	chr12:12561000-12561800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:12561000-12561800	Weak transcription	Dnd41	blood
19	chr12:12561000-12562000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr12:12561000-12562000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr12:12561000-12562000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr12:12561000-12562000	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr12:12561000-12562000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:12561000-12562200	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr12:12561200-12561600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:12561200-12562000	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr12:12561200-12562000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr12:12561200-12562000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:12561200-12562200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:12561400-12561600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:12561400-12561600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:12561400-12561600	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr12:12561400-12561600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:12561400-12561600	Enhancers	Brain Substantia Nigra	brain
35	chr12:12561400-12561600	Flanking Active TSS	GM12878-XiMat	blood
36	chr12:12561400-12561600	Enhancers	HSMMtube	muscle
37	chr12:12561400-12562000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr12:12561400-12562000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr12:12561400-12562000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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